Methods for designing and preparing vaccines comprising directed sequence polymer compositions via the directed expansion of epitopes

ABSTRACT

The instant invention comprises a process of preparing a composition comprising directed sequence polymer (DSP) mixtures that act as epitopes and useful as vaccines, such DSP synthesized according to a set of rules regarding the identity and the frequency of occurrence of amino acids that substitute a base or native amino acid of a known epitope. The resulting composition is a mixture of related peptides for therapeutic use as a vaccine, preferably for infectious agents that are immune evasive.

RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application 60/999,284 filed Oct. 16, 2007, and U.S. Provisional Application 61/124,689, filed Apr. 17, 2008.

FIELD OF INVENTION

This application provides methods of making improved compositions of peptide vaccines and provides methods of overcoming attenuated and inadequate immune responses associated with immune evasion.

BACKGROUND OF THE INVENTION

The infection of a host by an infectious pathogen is a complex event comprising a series of coordinated events in which the pathogen attempts to evade both the host's innate and adaptive immune systems. In their attempts to replicate and survive, the invading pathogens cause damage to the host. The destruction generally takes the form of cell death, either from pathogen entry into the cell or from endo/exo-toxins produced by the pathogen, as well as the induction of host cellular responses that have the ability to cause further tissue damage, scarring or hypersensitivity. Although between 1938 and 1952, the decline in infectious disease-related mortalities decreased 8.2% per year (Armstrong, G L et al., JAMA 1999, 281:61-6), the death rates due to infectious disease have been increasing since the 1980s. A study performed at the National Center for Infectious Diseases demonstrated that the death rate due to infectious diseases as the underlying cause of death increased 58% from 1980 to 1992. In 1992, 64 of every 1,000 deaths were attributable to infectious disease (Pinner, R W et al., JAMA 1996, 275:3).

The mechanisms of infectious diseases comprise two distinct but interconnected aspects: (1) the various organisms attempting to invade a host, each different class of infectious agents having distinct means by which they attempt to evade the host's immune system, and (2) the host's immune response to the invading pathogen. Humans have warded off infectious diseases in both of these aspects, in the first aspect, by preventing the access of infectious agents (e.g. by sanitary habits) and in the second aspect, by assisting and boosting the immune system by, for example, vaccination.

The Fight Against Infectious Disease

Immunization programs in the effort to control infectious diseases, such as small-pox, polio, measles, mumps, rubella, influenza caused by Haemophilus influenza (flu), pertussis, tetanus, and diphtheria, used centuries old technology to safely create an immune response in a host prior to pathogenic infection by the live organism. These vaccination protocols called for the introduction to the host of an inactive or very weak form of the actual pathogen, and in so doing an active immune response was created.

To make vaccination more effective, advances in eliciting stronger immune responses have been made with the development of antigen/epitope non-specific treatments that boost immune activity, such as the adjuvant alum (see Vaccine Adjuvants and Delivery Systems, edited by Manmohan Singh 2007 Wiley & Sons ISBN: 978-0-471-73907-4, incorporated by reference herein, for an extensive review of vaccine adjuvants), as well as development of immunogens based on the understanding of the genetic basis of these pathogens (GenBank, a database managed by the National Center for Biotechnology Information, now has over 85 billion base pairs in its database. Searching based on pathogen is widely used (http://www.ncbi.nlm.nih.gov/Genbank/). The latter has opened up the possibility of utilizing discrete sequences of proteins derived from the pathogen as immunizing agents in the context of cell-mediated (T cell via MHC class I and/or II), but not humoral (Bcell/antibody-mediated immunity). These peptide-based vaccines are specific to epitopes (also called antigenic determinants) that are the precise moieties within antigenic materials to interact with immune system components, intended to boost immune reactivity, and are administered using methods designed to excite immune function. One major limitation of the epitope/peptide-based approach is the variability with which the human MHC class I and II receptors bind the peptides.

While improvements to the techniques have been made in the form of differing types of inactivation of pathogen or in the use of adjuvants to enhance immunogenicity, there remain infectious diseases that are generally refractory to traditional vaccine therapies. In the context of influenza vaccines specific for a particular strain of the virus, clinical efficacy rates range near 40% when there is not a match with the circulating strain (Ben-Yedidia, T and Amon, R, Expert Rev. Vaccine 2007, 6:939-948).

A need remains in the development of vaccines that can handle the infectious agents such as human immunodeficiency virus (HIV), cytomegalovirus, and severe acute respiratory syndrome coronavirus, as well as bacteria such as Pseudomonas aeruginosa, Neisseria gonorrhea, or Mycobacterium tuberculosis or parasitic diseases such as malaria or hookworm disease. In the context of influenza, the current licensed vaccines are produced in eggs, and make use of half-century old technology (Ben-Yedidia 2007, above).

These infectious agents, bacteria, and parasitic diseases are harder to treat using the inactive pathogen vaccine approach because of the organism's ability to evade host detection. The HIV or the flu virus has the ability to alter its immune profile multiple times in the amount of time less than a calendar year, progressively marginalizing the effectiveness of immunity gained by previous infection and/or even the most recently created vaccine.

In particular, flu viruses, which can easily spread widely and ubiquitously throughout the world, have a large adverse effect on the human population, affecting 10-20% of the total world-wide population (Ben-Yedidia 2007, above). Flu viruses are categorized into three types, A, B, and C. Influenza C rarely infects humans, but influenza A viruses infect various species and B viruses are specific to humans. A and B can be highly virulent. The human immune system attacks flu viruses by targeting their surface proteins hemagglutinin (HA) and neuraminidase (NA). As such, subtypes of flu viruses are categorized as combination of HA type and NA type. HA is a tri-valent viral glycoprotein with two subunits H1 and H2. The virus uses the H1 portion to gain entry to host cells by binding to α2-6 linked sialosides (human), or 2-3 linked sialosides (avian) (Stevens, J et al., J. Mol. Biol. 2008, 381:1382-1394). The secondary and tertiary structures of HA have been solved (Wilson, I A et al., Nature 1981, 289:366-73). Currently there are 15 known subtypes of HA and 9 known subtypes of NA.

The difficulty for the human body to effectively counter influenza infection lies in the fact that the HA protein mutates quickly, allowing the viruses to evade the host organism's immune system. The average rate of amino acid substitutions is 3.6 per year (Smith, D J et al., Science 2004, 305:371-6). Once a mutation occurs in a given epitope region of influenza HA, a second mutation does not immediately occur in that epitope region resulting in a linear profile of temporal appearance of mutation sequence clusters in HA (Plotkin, J B et al., Proc. Nat. Acad. Sci. USA 2002, 99:6263-68). The H1 subunit of HA has been shown to have five main antigenic epitopes. In these regions the amount of mutation is significantly higher than in other regions of the protein.

It is important to understand the metes and bounds of the immunity induced in a host by immunization with a single strain of influenza; how said host responds to another strain dictates the selection of the next vaccine strain. The mutations in the influenza HA protein are subdivided into two groups, antigenic drift and antigenic shift. Antigenic drift is a phenomenon where the protein sequence of HA changes, resulting in immune evasion and improved ability of the virus to enter and replicate in a host cell. Drift measurement metrics have evolved and include the Hamming and Miyata metrics (Miyata, T et al., J. Mol. Evol. 1979, 12:219-36; Henikoff, S et al., Proc. Nat. Acad. Sci. USA 1992, 89:10915-19). Antigenic drift causes the seasonal flu surge that is usually not lethal to otherwise healthy people with normal immune system, but it still affects 10-20% of the world's human population, with up to 5 million cases of serious illness and half million deaths, according to the World Health Organization (WHO). Using the Hamming metric, investigators have suggested that no viral cluster (drifted sequences) has members that last longer than seven years, due to new dominant clusters that replace one another on average every 2-5 years. Other investigators have characterized the inter-pandemic evolution of influenza as intervals of immunologically neutral sequence evolution without significant antigenic alteration. During this time of stasis, there is a slow extinction of coexisting virus lineages that is contrasted with rapid and dramatic excess of amino acid replacements in the variable, or epitopic regions of HA, resulting in the ascension of the new dominant strain at the expense of the earlier variants (Wolf Y I et al., Biology Direct 2006, 34:1-19). These investigators determined that in periods of slow extinction (drift), the ratio of the number of amino acid replacements in the variable, or epitopic regions to the non-variable regions was 9:8, whereas periods of rapid extinction (shift) saw a ratio of 23:1 (Wolf, 2006, above). Thus one means to define a cluster of variants is those currently existing strains that have a ratio smaller than 9:8 of amino acid changes between epitopic and non-epitopic regions.

Antigenic shift, on the other hand, is a major change, requiring four or more amino acid changes across two or more antigenic sites (Plotkin, 2002 above). Such antigenic shift causes an increase in pathology and mortality in humans because of their immunological naiveté to the new strain. In the past, the fast expansions of Spanish flu or Hong Kong flu were deadly. Recently a threat of the H5N1 strain, the “bird flu” more fully described below, turning into a human pandemic strain is emerging.

The modern world has combated influenza epidemics by attempting to predict the next prevalent viral subtype and vaccinating people against it. In 1952, the WHO established the Influenza Program to assist fight against influenza epidemic, and coordinates a network of over 100 influenza surveillance centers all over the world. The centers characterize the antigenic properties of the isolated viruses using a test known as the hemagglutination inhibition (HI) assay, which measures the ability of the virus to agglutinate red blood cells, and the capability of antisera against related strains to inhibit such agglutination. The results of the HI assay is measured in units called antigenic distances, each of which unit corresponding to a twofold dilution of anti-sera in the assay (Smith, 2004, above). Thus a subsequent means to identify a cluster of variants is those currently existing strains having less than a twofold dilution of anti-sera in the HI assay.

In the United States, the Vaccines and Related Biological Products Advisory Committee of the Division of Viral Products (“the Vaccines Committee”) at the Center for Biologics Evaluation and Research (CBER) of the Food and Drug Administration defines the most relevant strains for the production of vaccines using the HI assay. When the antigenic distance is greater than two, the Vaccines Committee will update the variant for the upcoming season (Smith, 2004, above). For the Northern Hemisphere's 2008-9 season, for example, the Vaccines Committee recommended H1N1 A/Brisbane/59/2007 and H3N2 A/Brisbane/10/2007 for Influenza A and B/Florida/4/2006 for Influenza B for the seasonal production of licensed vaccines (inactivated or attenuated viruses).

The choice of the Vaccines Committee of which is the appropriate strain for the upcoming season's vaccine production and distribution is based in large part on antigenicity. Quantitative measurements of antigenic data include numerical taxonomy or its equivalent (Papaud, A, Poisson A, J Mar Res 1986, 44:385; Mecking S, Warner J, Geophys Res 1999, 104:11087), the method of Lapedes and Farber (Wallace D W R, Ocean Circulation and Climate Academic Press San Diego, Calif. 2001 pp 489-521) which uses ordinal multidimensional scaling in the interpretation of binding data so that an antigenic map, or the distance between an antigen and antiserum can be visualized. A refinement of the Lapedes and Farber method (Smith D J, 2004, above; Sabine C L et al., Global Biogeochem Cycles 16:1083, 2002) positions/overlays the antigens and the antisera on a map.

An alternate approach of defining clusters is differentiation by the organization of genetic (DNA) data into phylogenetic trees. The international surveillance programs are responsible for the majority of the sequencing performed in order to identify serologically novel influenza strains (Layne S P, Emerg. Infect. Dis. 12:562-68, 2006). Investigators have reported that the meaningful antigenic changes that occurred in an H3N2 subtype influenza virus during the period between 1983 ad 1997 were found predominantly in the internal and not external branches of the tree (Bush, R M et al. Mol Biol Evol 1999, 16:1457-65). Thus a further subsequent means to identify a cluster of variants is the branching organization of those currently existing strains obtained using genetic data.

There are various types of vaccines available for human use: DNA-based, cellular, live pathogen, attenuated or inactivated pathogen-based, recombinant protein and peptides. There are currently five inactivated seasonal vaccines for human use (Fluzone®, Fluvirin®, Fluarix®, FluLaval®, and Afluria®), and one live attenuated (FluMist®). Peptide based vaccines can be either recombinant or synthetic. Since 1993 there have been over 1,000 peptide based vaccines in pre-clinical research, over 100 in Phase I human clinical trials, a small few in Phase II, and none passing Phase III (Hans, D et al., Medicinal Chemistry 2006, 2:627-46).

The candidate viral subtypes for annual flu vaccine update do not include the mainly avian infective H5N1, which have historically infected poultry. However, investigators at Scripps Research Institute and others have identified the Egret/Egypt/1162/NAMRU-3/06 as a variant having likely human infective potential (Stevens, 2008, above). In fact, reports of the H5N1 viruses infecting humans are increasing. Because of the lack of exposure to related sub-strains, an H5N1 infection in a human often has severe effects. The recently emerging ability of the virus to infect humans is thought to be attributable to the conversion from a SAα2-3Gal to SAα2-6Gal receptor recognition by the virus. Investigators have found that H5N1 virus that infected humans is capable of recognizing both types of receptors (Yamada, S et al., Nature 2006, 444:378-82).

Although helpful to an extent in preventing the disease, the success of the WHO's Influenza Program is limited for several reasons. One such reason is the limited number of surveillance locations and a small sampling size compared to the occurrence of influenza infection (in 2004-2005, about 6000 samples, or 1 sample per 100,000 cases). Another drawback is the time it takes to prepare vaccines once such candidate antigenic subtypes have been selected (Layne, Emerging Infectious Disease 2004, 12(4): 562-568). Added to the difficulties is the above-mentioned antigenic drift and shift. New strains may appear at any time.

Another complicating phenomenon is broadening of the immune response via the process of epitope spreading, where a host's immune system over time changes target of the immune attack to nearby epitopes (N. Suciu-Foca et al., Immunol. Rev. 1998, 164:241). Thus, the inability to modulate the relevant antigenic determinants over time renders simple vaccines ineffective in a short time.

Therefore, a new method for developing and preparing vaccines that are effective under these circumstances are needed.

Strategy for Creating Active Peptides

In recent years, vaccines based on synthetic peptide epitopes rather than whole antigenic molecules have been explored and developed, in the hope of more refined targeting and ease of achieving consistent quality, as well as the safety of being non-infectious. The results are mixed. As a practical matter, it is time- and resource-intensive to identify one peptide or a set of a limited number of peptides that would be effective as a vaccine. In addition, because of the infectious agents' immune evasion strategies briefly described above, peptide epitope-based vaccines have not overcome the shortcomings of traditional vaccines. Investigators have attempted to make use of conserved epitopes within the virus. These regions do not mutate, and thus represent an approach for the generation of broad-spectrum, peptide-based vaccines (Ben-Yedidia, 2007, above). These approaches using short peptides; however, the invoked immunity is T cell-based, requires adjuvant or carrier proteins (flagella) and lacks the proven pathogen fighting ability of preexisting antibodies (Zinkernagel, R M, Nobel Lecture Dec. 8, 1996).

The development and exploitation of combinatorial chemistry (CC) has propelled drug discovery. Drug discovery can be generalized into two major steps, lead generation and lead optimization. Oftentimes, a lead compound is identified that has some of the desired characteristics of a commercially viable therapeutic, but has shortcomings such as a low specific activity, toxicity, instability, etc. Thus, once a lead is identified, practitioners attempt to optimize the lead compound by testing other related compounds with similar structures. CC allows practitioners to create and quickly screen a library made of a vast number of candidates, to identify those with a specific activity against a target of interest.

For peptide based drugs, the goal is to define a single, or a limited set of peptides which demonstrate a particular activity. The art of CC as applied to the synthesis of peptide libraries, too, has advanced, producing highly reliable and pure mixtures of peptides of great diversity. The process of identifying the single or limited set of peptides that were responsible for the observed activity from such diverse libraries, called deconvolution, is schematically represented in FIG. 1A.

Drug discovery based on CC are powerful, but deconvolution can be difficult and time- and cost-intensive. Thus, to simplify deconvolution and make the process more efficient, practitioners have spent great efforts to create suitable synthesis methods. Examples of the resulting evolution of subtypes of combinatorial methods include: multiple synthesis, iterative synthesis, positional scanning, and one-compound-one-bead post assay identification design. They are briefly described below to show the state of the art and how peptide epitopes were successfully identified.

“Multiple synthesis” provides for any method whereby distinct compounds are synthesized simultaneously to create a library of isolated compounds. The identity of these compounds would be known from the rules of the synthesis. An example is found in H. M. Greysen et al., Proc. Nat. Acad. Sci. USA, 1984, 81:3998, where the investigators identified GDLQVL, out of 108 overlapping peptides, as the epitope recognized by an antibody raised against VPI protein of foot-and-mouth disease virus.

“Iterative synthesis/screening” involves methods of peptide synthesis which facilitates the determination of the peptide sequences as deconvolution is performed. This is done by synthesizing pools of peptides, each pool consisting of peptides with the two amino terminal residues defined and known to the investigators. These peptides can be shown as O₁O₂XXXX, wherein O1 and O2 are the defined residues and X is randomly selected. When a pool that contains a peptide that binds to a target is identified, the two amino terminal residues are known. The next step was to do the same for position three, by synthesizing peptides that can be shown as F₁F₂O₃XXX, wherein O3 is a fixed residue. Subsequent residues are determined in a similar manner. An example of iterative synthesis can be seen in R. A. Houghten et al., Nature 1991, 354:84-86, wherein the investigators honed in on the sequence DVPDYA as the core epitope after identifying YPYDVPDYASLRS using an ELISA type assay format.

“Positional scanning” is a synthesis method producing complex mixtures of peptides that allows for the determination of the activity of each individual peptide. Based on the screening results, the derived peptide can then be separately synthesized for optimization. As seen in C. Pinilla et al., Biochem J. 1994, 301:847-853, positional scanning libraries were used to identify decapeptides which bound the same YPYDVPDYASLRS-binding antibody. In this case ten different libraries each containing 20 pools with a defined amino acid at each of the ten positions in the peptide. Fifteen peptides were identified.

Each of the above methods were also employed to identify enzyme substrates (J. H. Till et al., J. Biol. Chem. 1994, 269:7423-7428, J. Wu et al, Biochemistry 1994, 33:14825-14833, W. Tegge et al., Biochemistry 1995, 34:10569-10577) or enzyme inhibitors (M. Bastos et al., Proc. Nat. Acad. Sci. USA 1995, 92:6738-6742, Meldal et al., Proc. Nat. Acad. Sci. USA 1994, 91:3314-3318, R. A. Owens et al., Biomed Biophys. Res. Commun. 1994, 181:402-408, J. Eichler et al., Pept. Res. 1994, 7:300-7).

As powerful and clear-cut the identification of a specific peptide may be, as a therapeutic, such identified peptide may only be a lead peptide that is not itself useful. The identified peptide epitope may be ignored by the immune system if it resembles a self protein or possibly exacerbate the very condition that the therapy aims to relieve. However, by designing peptides of similar sequence, one may create, based on such peptide, epitope reactive analogs that would act as modifiers of the immune responses and/or as excitors of an immunogenicity response.

One such approach is creation of altered peptide ligands (APL). This approach is schematically represented in FIG. 1B. An APL is defined as an analog peptide which contains a small, number of amino acid changes from a starting sequence such as that of a native immunogenic peptide ligand. While recognition of the native response may induce an antagonist-like reaction, an APL might also induce a partial agonist response, or induce a state of anergy in the reactive T cell population. In discussing APL in the context of allograft rejection therapy, Fairchild et al., Curr. Topics Peptide Protein Res. 2004, 6:237-44, note that an APL acting as an antagonist for one TCR, may become an agonist for another, complicating the rational design of an APL. Compounding the obstacle of the development of APL is the difficulty in translating a response developed in an animal system into human.

An illustrative example is an APL based on an epitope of myelin basic protein, MBP83-99 (ENPVVHEFKNIVTPRTP), which is reported to be a target of autoimmune response causing multiple sclerosis. APLs were made by replacing the bold and underlined amino acid residues “E”, “N”, “E” and “K,” resulting in identification of a single peptide having the amino acid residue sequence AKPVVHLFANIVTPRTP that appeared to have the desired activity of neutralizing antibodies against MBP83-99, Kim et al. Clinical Immunology, 2002, 104:105-114. The peptide was placed into limited human trials, which reportedly resulted in the long term immune reactivity against the peptide, but the treatment has been deemed clinically ineffective by evaluation using MRI. Thus an APL, once identified, can be used as a therapeutic agent; however, its effectiveness may be limited in terms of clinical efficacy.

Evasive Targets

In the context of developing vaccines in the prevention of infectious disease, the invading pathogens have acquired by natural selection the ability to quickly create variability in the relevant immunogenic epitope. Examples of viral mutants generating escape variants that avoid immune detection have been reported for Hepatitis B, influenza, and HIV (Tabor, E, Journal of Med. Virol., 2006, 78:S43-S47; Daniels, R S et al., EMBO Journal 1987, 6:1459-65; D'Costa, S et al., AIDS Res Hum Retroviruses 2001, 17:1205-9). This variation progressively dampens the utility of single-epitope vaccines.

Thus, investigators have attempted to overcome this limitation by introducing variance by creating a mixture of immunity-inducing epitopes to be used as vaccines. Furthermore, it has previously been shown that mixtures of related peptides may be therapeutically more effective than a single peptide. Lustgarten et al., J. Immunol. 2006, 176: 1796-1805; Quandt et al., Molec. Immunol. 2003, 40: 1075-1087. The effectiveness of a peptide mixture as opposed to a single peptide is the likelihood of interaction with the broadening of the relevant epitopes via evolution-induced variation. Therefore, to increase and maintain the longer-term effectiveness, these previous treatment modalities have been modified. For example, a therapeutic composition based on an APL may include multiple peptides created by the APL method in combination with the original peptide, or other APLs. Fairchild et al., Curr. Topics Peptide & Protein Res. 2004, 6:237-44. Each APL would have a defined sequence, but the composition may be a mixture of APLs with more than one sequence. A reverse example involving conceptually similar altered peptide ligands involves an inventor's attempt to reduce the amount of variation created by pathogens to avoid immune recognition (viral alteration of immunogenic epitopes over time, e.g., the creation of altered peptide ligands), by using the very changes created by the pathogen in an epitope sequence to create a limited diversity pool of peptides potentially useful in vaccinations (U.S. Pat. No. 7,118,874). In this invention, distinct hyper-Variable region sequences from HCV or influenza virus were compared. The amino acid changes having a frequency greater than 12% were incorporated into a mixture of between 2 and 64 different peptides.

However, a simple mixture of several soluble peptide epitopes faced certain manufacturing issue of soluble peptide mixtures, such as difficulties in delivering a consistent ratio and quantity of each of the peptides in the mixture.

Peptide dendrimers were conceived to overcome some of these shortcomings of soluble peptide mixtures, and also by providing other perceived advantages. This approach is schematically represented in FIG. 1C. The design of dendrimers intends to mimic two traits of naturally occurring biological structures: a globular structure and polyvalency to amplify the ligand:substrate interaction. Beyond these commonalities, dendrimers are chemically and structurally diverse, with reports of a wide range of sizes, from 2 kDa to greater than 100 kDa. Dendrimers are described in two comprehensive reviews (P. Niederhafner et al., J. Peptide Sci. 2005 December; 11(12):757-788; K. Sadler and J. P. Tam, Rev. Mol. Biotechnol. 2002, 90:195-229), and their applications in additional literature (D. Zanini and R. Roy, J. Org. Chem. 1998, 63:3468-3491; J. Haensler and F. C. Szoka, Bioconjug Chem. 1993, 4:372-379; Tam, James P et al., J. Exp. Med. 1990, 171:299-306).

Despite attempts and a certain amount of success in utilizing dendrimers and some improvements in synthesis and purification strategies, a high cost of manufacturing and the subsequent analytical development precludes this technology from being further currently developed commercially.

All of the above strategies, while recognizing the advantage of variations in the therapeutic peptide compositions, derive from the concept that there is one or more defined peptide sequences evoking a defined immunological response. These strategies have attempted to multiply and diversify modulatory peptides via the introduction of defined, single changes performed one at a time.

An entirely different approach which has evolved alongside the defined sequence peptide immunotherapy approach is the use of random epitope polymers. Random sequence polymers (RSP) can be described as a random order mixture of amino acid copolymers comprising two or more amino acid residues in various ratios, forming copolymers by random sequence bonding, preferably through peptide bonds, of these amino acid residues, which mixture is useful for invoking or attenuating certain immunological reactions when administered to a mammal. Because of the extensive diversity of the sequence mixture, a large number of therapeutically effective peptide sequences are likely included in the mixture. In addition, because of the additional peptides which may at any given time not be therapeutically effective, but may emerge as effective as the epitope shifting and spreading occurs, the therapeutic composition may remain effective over a time of dosing regimen. This approach is schematically represented in FIG. 1D.

Copolymer-1 (also known as Copaxone®, glatiramer acetate, COP-1, or YEAK random copolymer) is an FDA approved, commercially available therapeutic used for the treatment of multiple sclerosis comprising random copolymers of Y, E, A, and K. Random copolymers are described in International PCT Publication Nos. WO 00/05250, WO 00/05249; WO 02/59143, WO 0027417, WO 96/32119, WO/2005/085323, in U.S. Patent Publication Nos. 2004/003888, 2002/005546, 2003/0004099, 2003/0064915 and 2002/0037848, in U.S. Pat. Nos. 6,514,938, 5,800,808 and 5,858,964. It is one of the few therapeutics for multiple sclerosis that continues to be effective over time.

Attempts continue to build on the success of COP-1 by creating other RSPs and related peptide compositions. WO/2005/074579 (the '579 publication) describes complex peptide mixtures of various amino acid composition. The disclosure also contains diversity-constraining mechanisms of defining amino acids at certain positions rather than being chosen by the random nature of the synthesis rules. Another such attempt is the work originated by Strominger et al. (WO/2003/029276) and developed further by Rasmussen et al. (US 2006/0194725) wherein they created RSP consisting of the amino acids Y, F, A, and K with different amino acid ratios and a shorter average length than COP-1 Alanine content was increased based on Maurer (Pinchuck and Maurer, J. Exp Med 122(4), 673-9, 1965), which described how an EAK polymer with higher alanine content (10-60 mole percent) produced “better antigens”; Rasmussen et al. in fact demonstrated that a YFAK input ratio of 1:1:1:1 was not effective in eliciting a recall response as compared to a YFAK preparation with an input ratio of 1:1:10:6.

WO/2005/032482 (the '482 publication) describes another approach, which is to build degenerate peptide sequences based on motifs, exemplified by [EYYK]. The motifs are used as is, or can be altered by amino acid substitutions (defined on page 10-11 of the '482 publication). A significant difference from COP-1 is that it lacks alanine. Much of the invention hinges on the presence of a D-amino acid at the amino terminal of the motif.

Tracing back steps to the defined peptide search, there have also been attempts to identify the active peptide(s) within the RSP mixture. The drawback of this technology lies in the very nature of the attempt to determine discrete substitutes for the randomness that COP-1 encompasses.

Effective as the random sequence polymer approach may be, even the improvements have not resolved the drawback and limitation of COP-1, which is, for example, the undefined nature of what is effective in each motif and the possibility of containing a large proportion of truly inactive peptides, lowering the concentration of the active components, or worse, adversely stimulating the immune system. Additionally, these compounds are difficult to manufacture and to obtain consistency from lot-to-lot.

All these approaches have not overcome the shortcomings of previously existing systems, and need remains for a composition and a method to create such composition that would serve effectively as a vaccine by eliciting beneficial immune responses consistently and over time toward pathogens, for which existing vaccine compositions have failed to be effective.

SUMMARY OF THE INVENTION

The instant invention comprises a process for designing, manufacturing, and administering a composition comprising directed epitope peptide mixtures useful for eliciting immune responses in the up-regulation of immune function in the treatment of infectious disease, such process defined by a set of rules regarding the identity and the frequency of occurrence of amino acids that substitute a base or native amino acid of a known sequence, or epitope. A method of the instant invention uses a sequence of a known sequence, or epitope as a starting point. The amino acids that make up the epitope are modified via the introduction of different, related amino acids defined by a set of rules. The result is a mixture of related peptides useful in and of itself as a therapeutic, which is described herein as a composition comprising “directed-sequence polymers” or “DSP”. Such composition is referred to as a “DSP composition.” The method of synthesizing a DSP composition utilizes and maintains the natural order of amino acid residues of a defined peptide sequence of a specified length. Each amino acid position is subjected to change based on a defined set of rules. In a preferred embodiment the amino acid is substituted according to the methods described in Kosiol et al., J. Theoretical Biol., 2004, 228:97-106. Alternatively, amino acids can be changed in accordance with the exemplary substitutions described in PCT/US2004/032598, page 10-11. Alternatively, amino acids can be changed in accordance with the differences at a given position between variants within a given pathogen. Alternatively, amino acids can be changed in accordance with the differences at a given position between variants of sub-species of a given pathogen.

For the solid phase synthesis procedure of the instant invention, the mixture of amino acids for a given position in the peptide is defined by a ratio of one to another. Prior to starting the synthesis, such ratio is determined for each position along the peptide. The resulting directed order peptide mixture comprises a multiplicity of related peptide sequences.

The length of a DSP can be one of the original defined sequence peptide or, generally any length up to up about 30 repeated lengths of the original defined sequence peptide, but is dictated by the total length of the desired end product. The length of the full length of a DSP sequence can be between about 25 and about 300 amino acids, and preferably between about 45 and 70 amino acids.

When considering the entire length of a DSP, the percentage of alanine as compared to all of the other amino acids in the DSP combined is greater than 5% on average, and will not exceed 90% on average. Preferably, the alanine percentage is between 10% and 70% on average. More preferably the percentage of alanine is between 15% and 35% on average.

When considering a “cassette” comprising the DSP that is less than the entire length of the DSP, the percentage of alanine as compared to all of the other amino acids in the section of the DSP will always be greater than 1% on average, and will not exceed 99% on average. Preferably, the alanine percentage is between 5% and 95% on average. A cassette is a synthesis unit of DSPs with a defined relative amino acid ratio, and comprises a sequence of an identified epitope.

The complexity of the mixture is greater than 5×10² different peptides. In a further embodiment, the complexity of the mixture is greater than 1×10⁴ different peptides. In a further embodiment, the complexity of the mixture is greater than 1×10⁶ different peptides. In a further embodiment, the complexity of the mixture is greater than 1×10⁸ different peptides. In a further embodiment, the complexity of the mixture is greater than 1×10¹⁰ different peptides. In a further embodiment, the complexity of the mixture is greater than 1×10¹² different peptides. In a further embodiment, the complexity of the mixture is greater than 1×10¹⁴ different peptides.

In some embodiments, the base peptide sequence from which the DSP sequences are derived is selected from a group consisting of SEQ ID NO: 1-7 depicted in Table I.

In other embodiments, such base peptide sequence is an epitope relevant to the pathology of a viral infectious disease selected from the group consisting of AIDS, AIDS Related Complex, Chickenpox (Varicella), Common cold, Cytomegalovirus Infection, Colorado tick fever, Dengue fever, Ebola haemorrhagic fever, Hand, foot and mouth disease, Hepatitis, Herpes simplex, Herpes zoster, HPV, Influenza (Flu), Lassa fever, Measles, Marburg haemorrhagic fever, Infectious mononucleosis, Mumps, Poliomyelitis, Progressive multifocal leukencephalopathy, Rabies, Rubella, SARS, Smallpox (Variola), Viral encephalitis, Viral gastroenteritis, Viral meningitis, Viral pneumonia, West Nile disease, and Yellow fever.

In particular, the present invention is well suited for developing and preparing influenza vaccines. Exemplary sequences of influenza HA protein are SEQ ID NO: 8-16, from which partial sequences can be selected based on further examples described herein as epitopes and thus as the base sequences for the present invention.

In other embodiments, such base peptide sequence is an epitope relevant to the pathology of a bacterial infectious disease selected from the group consisting of Anthrax, Bacterial Meningitis, Botulism, Brucellosis, Campylobacteriosis, Cat Scratch Disease, Cholera, Diphtheria, Gonorrhea, Impetigo, Legionellosis, Leprosy (Hansen's Disease), Leptospirosis, Listeriosis, Lyme disease, Melioidosis, MRSA infection, Nocardiosis, Pertussis (Whooping Cough), Plague, Pneumococcal pneumonia, Psittacosis, Q fever, Rocky Mountain Spotted Fever (RMSF), Salmonellosis, Scarlet Fever, Shigellosis, Syphilis, Tetanus, Trachoma, Tuberculosis, Tularemia, Typhoid Fever, Typhus (including epidemic typhus), and Urinary Tract Infections.

In other embodiments, such base peptide sequence is an epitope relevant to the pathology of a parasitic infectious disease selected from the group consisting of Amoebiasis, Ascariasis, Babesiosis, Chagas Disease, Clonorchiasis, Cryptosporidiosis, Cysticercosis, Diphyllobothriasis, Dracunculiasis, Echinococcosis, Enterobiasis, Fascioliasis, Fasciolopsiasis, Filariasis, Free-living amoebic infection, Giardiasis, Gnathostomiasis, Hymenolepiasis, Isosporiasis, Kala-azar, Leishmaniasis, Malaria, Metagonimiasis, Myiasis, Onchocerciasis, Pediculosis, Pinworm Infection, Plasmodium, Scabies, Schistosomiasis, Taeniasis, Toxocariasis, Toxoplasmosis, Trichinellosis, Trichinosis, Trichuriasis, Trichomoniasis, and Trypanosomiasis (including African trypanosomiasis).

Another embodiment of the invention is based on the base peptide sequence relevant to prion-diseases. SEQ ID NO: 17 is human prion protein sequence. A relevant peptide is selected from partial sequences of SEQ ID NO: 17.

Another aspect of the invention is a process for preparing a composition comprising DSPs described above, wherein the naturally occurring immune response is inadequate for preventing or overcoming the pathology associated with the epitope for which the immune response is elicited.

One aspect of the present invention is a pharmaceutical composition comprising a DSP composition, optionally as a pharmaceutically acceptable salt. In a preferred embodiment, such pharmaceutical composition comprising a DSP composition, when administered to a subject, causes a favorable modification of otherwise limited and inadequate immune response in the subject desirous of such a modification, such as an increase in appropriate immune responses.

Another aspect of the present invention is a method of enhancing immune responses by administering a DSP composition to a subject in need thereof. In a particular embodiment, the subject exhibits only a limited and inadequate immune response to undesirable pathogens. In certain embodiments, the subject is in need of such administration because of an infectious disease or similar disorder that can be recognized by one of ordinary skill in the art. Another aspect of the present invention is a method of treating a diminutive immune response by administering a DSP composition comprising base peptide sequences that are unrelated to the pathogen of interest and that are useful in boosting generalized immune function.

Yet another aspect of the invention is a method of protecting a subject from an influenza infection wherein the influenza virus is a new immunologic subtype comprising the step of administering a pharmaceutical composition comprising a DSP composition the base sequence of which comprises an epitope from hemagglutinin of an influenza virus subtype that caused the most immediate past epidemic at any given time when such protection is desired. The new immunologic subtype may be an antigen drift or antigen shift.

A still further embodiment of the instant invention is a method of designing, manufacturing, and administering a vaccine directed against all the variants of the most recently dominant cluster of related influenza virus. Said virus may derive from influenza A, B, or C, and may be influenza A subtype H3N2, H1N1, or H5N1 or a future shifted variant thereof.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A-D is a schematic depicting methodologies for designing synthetic peptide-based therapeutics. Panel A: how a peptide library is used for epitope discovery; Panel B: conceptual steps for generating Altered Peptide Ligand-based therapeutic; Panel C: a schematic of a dendrimer for multi-valent peptide presentation; Panel D: random sequence polymer generation.

FIG. 2 is a schematic for conceptual steps for generating Directed-Sequence Polymers.

FIG. 3 shows the steps for preparing Directed-Sequence Polymers.

FIG. 4 shows the preferred defined substitutive rules for directed expansion of epitope permeability.

FIG. 5 shows a generic rule structure and ranges of substitutions of DSP synthesis.

FIG. 6 shows an example of the application of the DSP Synthesis Rules using a mock-source peptide.

FIG. 7A-E shows examples of the application of the DSP Synthesis Rules using influenza epitopes as source peptides.

DETAILED DESCRIPTION OF THE INVENTION

The instant invention draws out the most useful properties of the previous treatment modalities yet removes the limitations of each. The instant invention utilizes: (1) the specific immunologic relevance of a defined epitope peptide, (2) the modulatory properties of an APL, (3) the desirable multivalency, (4) and the alanine content from RSP to generate a directed expansion via alteration and degeneration of epitope variability that forms a complex yet directed peptide library useful for delivery as a vaccine. The approach is schematically represented in FIG. 2.

The instant invention relates to a “Directed-Sequence Polymer” (DSP). A DSP is a peptide within a library of related peptides having a sequence derived from a base peptide sequence, which may be but not limited to a native epitope associated with a desired immune response. A DSP has one or more amino acid residue that differs from that of the base peptide sequence, the substitution of which is determined by a defined rule. A DSP composition comprising multiple DSPs is synthesized by applying a set of synthesis rules that define the amino acid variations and the ratio of occurrence of introduction of such amino acid residues at any given position of the sequence to the base peptide sequence. Thus, a DSP is not synthesized as a single peptide, but is always synthesized as part of a composition comprising multiple related DSPs, the overall mixture of which is reproducible and consistent with the rules of synthesis that were applied. The schematic for the steps for creating a DSP composition, starting from the choice of a base peptide, is shown in FIG. 3.

I. Base Peptide Sequences

To create a meaningful DSP composition, one first needs to define the base peptide sequence to derive the DSPs from. The base peptide sequences can be derived in many ways. A peptide sequence useful for this purpose is a peptide sequence related to immune response in a mammal. Alternatively, the base peptide sequence can be derived from the group consisting of a virus, bacteria or parasite. Further examples of peptide sequences are, for example, empirically derived peptide sequences, such as through screening of library created by combinatory chemistry.

Infectious Disease-Derived Base Peptide Sequences

As briefly touched in the Background section, the use of vaccines to combat infectious diseases has been the classic paradigm of immunotherapy. However, not all known and significant infectious agents are readily treated with vaccines created by conventional methods. Epitopes that are therapeutically and prophylactically effective may be cryptic, or they may change so frequently as to render a developed vaccine ineffective and irrelevant. Rapidly evolving viruses would mean the number of people carrying the virus with same immunological profile becomes small, fragmenting the patient population against which a vaccine may be effective. Moreover, chronic infections caused by agents such as HIV, hepatitis C virus (HCV), and human papillomavirus (HPV) may require a different approach to immune elicitation due to the fact that they evolved to evade immune systems and are poor antigens.

As described in the Background section, one of the most evasive infectious agents is the influenza virus. The humoral human immune system recognizes two major immunogenic proteins from the virus, hemagglutinin (HA) and neuraminidase (NA). The known epitope regions of the head or top of the HA molecule correspond to the hypervariable regions These sequences are highly mutable and in fact isolated sequences have variations within this region.

Another epitope thought to be potentially useful as a target for flu vaccine is the extracellular peptide M2e of the integral M2 protein, conserved in all influenza A strain. Ben-Yadidia, T. and Amon, R., 2007, Expert Rev. Vaccines 6(6):939-948.

Current therapeutic regimens for HIV treatment comprise immunization using clade B gag, protease, reverse transcriptase, gp120 and nef peptides and lipopeptides, both by expression of these proteins using expression vectors and by direct immunization. Other immunogenic and therapeutically promising HIV proteins are gp41 and env proteins.

Unlike Hepatitis A and Hepatitis B, for which there are effective vaccines and antibody treatments available, Hepatitis C has evaded immune responses. Vaccines based on envelope glycoprotein (E1/E2) and virus-like particles have met limited success.

The peptide sequences of these proteins and epitopes have been extensively investigated and are readily available to one skilled in the art. See, for example, Berzofsky et al., J. Clin. Invest. 114:450-462 (2004) for a review with citation of these proteins. Further, Immune Epitope Database and Analysis Resources (http://www.immuneepitope.org), particularly useful for obtaining data and analysis of influenza HA and NA proteins.

Examples of epitopes identified as part of a naturally occurring, full length protein or synthetic peptides that were identified to have similar activities as such epitopes are shown in the table below.

TABLE I Examples of epitopes Source/Original Residue SEQ  Peptide Sequence Protein Number Ref ID NO: ILARNLVPMV human 491-500 1 1 cytomegalovirus HCMVpp65 ELEGVWQPA HCMVpp65 526-534 2 RIFAELEGV HCMVpp65 522-530 3 NLVPMVATV HCMVpp65 495-503 4 RIQRGPGRAFVTIGK HIV-gp120 V3 loop 2 5 IIPKSSWSDHEASSGVSSACPYQ Influenza virus HA 115-240 3 6 GRSSFFRNVVWLIKKDNAYPTIK protein H5 Accession RSYNNTNQEDLLVLWGIHHPNDA Number ACD62257 AEQTRLYQNPTTYISVGTSTLNQ RLVPKIATRSKVNGQSGRMEFF WTILKSNDAINF CIIPKSSWSDHEASSGVSSACPY Influenza virus HA 115-163 7 QGRSSFFRNVVWLIKKDNAYPTI protein H5 Accession flanked by KRSYC Number ACD62257 cysteines

Empirically Derived Base Peptide Sequences

As described in the above sections, peptide sequences with some significance to a disease state or an adverse reaction may be identified through experimental investigation of a relevant epitope. These sequences may include non-naturally occurring peptide sequences that proved to be useful in treating a disease or a condition, an example found in the international patent application publication WO 2006/031727, U.S. Pat. No. 6,930,168 and the related scientific publication by Stern et al., Proc. Nat. Acad. Sci. USA, 2005, 102:1620-25.

Further, epitopes are empirically determined by identifying candidate sequences by positional scanning of synthetic combinatorial peptide libraries (see, for example, D. Wilson et al., above; R. Houghten et al., above; Hernandez et al., Eur. J. Immunol., 2004, 34:2331-41), or by making overlapping peptide sequences of the entire protein of interest, and testing those peptides for immune reactivity using, for example, any readout assay useful for such purposes, such as the HI assay, a viral challenge model, or one described in Current Protocols in Immunology Edited by John E Coligan, Ada M Kruisbeek, David H Margulies, Ethan M Shevach, Warren Strober NIH, John Wiley & Sons, in an in vitro or in vivo assay system appropriate for the disease and species the epitope is sought for. Candidate molecules may include peptides that are modified during or post-synthesis by, for example, sugar- and modified sugar addition such as glycosylation and glycogenation either N or S-linked, fatty acid modification such as myristoylation, or containing disulfide bonds.

After identifying a candidate epitope, a probable set of additional related epitopes are generated using sub-strain variants, cluster variants, drift variants, shift variants of a pathogen, or via modeling and prediction algorithms described in readily available references, for example WO 2000/042559, align and analyze the mutations, probable anti-body accessible epitopes, or predicted binding of these probable epitopes using available prediction methods described in, for example, WO 2005/103679, WO 2002/073193 and WO 99/45954. Selecting from the peptides having the highest predicted activity/binding, take 40% of the predicted sequences and acquire the percentage of any given amino acid at each position. Use those percentages to create the rules for amino acid incorporation into a DSP synthesis.

II. Rules of Synthesis for Directed-Sequence Polymers

Steps in the creation of a DSP sequentially encompass the following:

(a) Identify a protein having known or believed association with a pathology.

(b) Select from within the protein a peptide or peptides, each having a fixed sequence, that are associated with the pathology and immunologically relevant. If no peptides have been described, then peptides useful in the treatment of the pathology of interest are created. One exemplary method is to create a library of peptides that collectively span the entire length of the protein of interest. This may be done by, for example, partial endopeptidase digestion or by peptide synthesis. The peptides may be further chemically modified by, for example, sugar- and modified sugar addition such as glycosylation and glycogenation, fatty acid modification such as myristoylation, or introducing disulfide bonds. The library is screened for immunologically relevant peptides using appropriate detection methods such as the functional assays HI, or viral challenge, or via binding affinity determination using antibodies detected in the sera of patients with the target pathology. The peptides may be further examined for immunogenicity useful for the treatment of the pathology in an in vitro or in vivo experimental system.

(c) the amino acid substitutions are decided based on either of two sets of rules, defined or empirical, and are set forth below;

(d) Solid phase synthesis of DSP according to the rules is performed, and pharmaceutically acceptable formulation the DSP is delivered as a vaccine.

The rules of synthesis for a composition comprising DSPs are outlined below. Briefly, a DSP may be envisioned as a polypeptide having a defined length that is either the same length as or multiples of the length of the base peptide sequence. For selected residue positions of the base peptide sequence, one or more substitute residue is defined. The rule of synthesis defines the ratio among the original base peptide residue for that position, the first substitute residue, the second substitute residue, the third substitute residue, the fourth substitute residue, the fifth substitute residue, the sixth substitute reside, and an alanine, to occupy any given residue position.

The substitute residues are defined: (1) according to a rational comparison and finding of similarities of relevant characteristics of the original residue with those of the substitute residue, (2) in accordance with the differences at a given position between species (including, in case of microbes, “serotypes” and “immunological subtypes”, (3) in accordance with the differences at a given position within variants of the same species, or (4) to a comparison of reported experimental results on the relative activities of actual peptides having slight variations from the base sequence. The substitute residues defined in any of these approaches are termed “conserved substitution” herein.

An example of a rational comparison and findings of similarity is the methods described by Kosiol et al., J. Theoretical Biol., 2004, 228:97-106. Amino acids are grouped together in a matrix, referred therein as PAM replacement matrix. FIG. 4 is a table showing the amino acid similarity and grouping, according to Kosiol, based on the characteristics of the residues such as size, charge, hydrophobicity, etc. In FIG. 4, amino acids grouped together are considered interchangeable, with high likelihood of retaining characteristics common among the group,

A comparison of experimental results showing the relative activities of peptides having slight variations from the base sequence can also be used as a basis for the rule for substitution. The sequences of the peptides responsible for observed changes are aligned and the type and percent presence of the new amino acid are noted. If there is more than one amino acid substitution at any given position of the peptide, the frequency of occurrence of an amino acid and the magnitude of activity change compared to the original sequence are taken into account to determine the order of prevalent substitution. Examples of the overall process leading up to the rule generation for DSP synthesis can be found using libraries (Molec. Immunol. 40:1047-1055; Molec. Immunol. 40:1063-74; J Autoimmunity 20:199-201; and J. Immunol. 163:6424-34), by making altered peptide ligands of overlapping peptides representing the entire protein of interest (Atkinson et al., J. Clin. Invest. 94:2125-29; Meini et al., J. Clin. Invest. 92:2633-43) or de novo (U.S. Pat. Nos. 7,058,515; 6,376,246; 6,368,861; 7,024,312; 6,376,246; 7,024,312; 6,961,664; 6,917,882). Briefly, a cellular material of interest is chosen as the assay system to rank the immunoreactivity of the peptides to be interrogated. Such an assay system can be either an in vitro or in vivo system, and can comprise adaptive or innate immune reactivity. Readouts for the assay system can be the up- or down-regulation of the status of the activation state of a protein, a change in the localization of a protein, the expression of the mRNA encoding for the protein, the relative concentration of a protein, changes in the generation of specific cell types, changes in cellular phenotype, changes in cellular activation, changes in cell number, changes in organ size or function, changes in animal behavior or phenotype, hemagglutination of red blood cells, or survival. Once the assay or assays are performed the results are analyzed to determine the prevalence of any particular amino acid as a conserved substitution. If more than six residues in a given position within the peptide sequence are identified as generating a change in immunologic function, the top six residues first by frequency of representation in the interrogated peptides, and second by the magnitude of changes elicited. Once chosen, the relative amounts of the residues are defined. As depicted in FIG. 5, each cassette, “y”, has a set of amino acid ratios one to another that have a range of about 0-100 for the base (a), the primary change (b), the secondary change (c), and the tertiary change (d), whereas alanine (e) has a ratio of about 0.5-100.0. If existing or desirable number of changes are larger, quaternary and further advanced changes up to 10 amino acids may be incorporated. The rules for the DSP synthesis continue with the combination of the cassettes in the order prescribed. The same block can be repeated either sequentially or separated by another block. On either side of the cassette sequence are N- and C-terminal modifiers. The number of cassettes is dictated by the requirements of the end length of the DSP which is required to be longer than 25 amino acids and shorter than 300 amino acids. Preferably, the full length of the DSP is between about 30 amino acids to 150 amino acids. More preferably, the full length of the DSP is between about 45 amino acids to about 70 amino acids.

As described in FIG. 6, the instant invention envisions multiple epitopes to be defined as separate cassettes and synthesized sequentially. Cassette ratios within the same DSP may have different ratios of amino acids. Further, if there are less than three non-alanine amino acid substitutions, the percentage of the ‘missing’ substitution is added to the base sequence. Further, a cassette may be placed in any order with multiple appearances in the overall DSP synthesis. The N- and C-terminal modifications reside prior to and after the entirety of the DSP cassettes respectively. As seen in FIG. 7A, a single base peptide sequence may have more than one ratio defined as a separate cassette in this example y1, y2, and y3. The individual cassettes can be placed in any order with multiple appearances in the overall DSP synthesis as seen in FIG. 7B.

A cassette may be repeated more than once. After a desired number of multiples of the cassette, if the desired length of the DSP is not yet reached, the DSP sequence is further defined by applying the same process, possibly using different ratio among the original, substitute, second substitute, and alanine residues.

N or C-terminal DSP modifiers may be added to the synthesis rules. The purpose of such modifiers include but are not limited to enhancing immunogenicity such as KLH, ovalbumin or bovine serum albumin, enhancing binding to specific proteins as in the case of RDG-based amino acid sequences (U.S. Pat. Nos. 5,773,412; 5,770,565) used as targeting moieties, or peptides that are known to bind to a wide array of HLA-DR species, such as AKAVAAWTLK AAA (U.S. App. Pub. No. 2006/0018915) as a DR-targeting moiety. Such modifiers may include moieties which enhance complexation to delivery systems including sustained release delivery systems. Modifiers can be resorbable matrix constructs/synthesizable backbones such as PLGA. Modifiers can be protease resistant moieties such as D-amino acids.

Thus, for any given base peptide sequence, a set of synthesis rules is applied to yield a composition comprising reproducible, consistent mixture of DSPs.

III. Peptide Synthesis Methods

Any known solid phase synthesis appropriate for peptide synthesis may be used to synthesize a composition comprising DSPs, for example as originally described by Merrifield (J. Am. Chem. Soc., 1963, 85:2149) and any variation thereof. More specifically, the synthesis is done in multiple steps by the Solid Phase Peptide Synthesis (SPPS) approach using Fmoc protected amino acids. SPPS is based on sequential addition of protected amino acid derivatives, with side chain protection where appropriate, to a polymeric support (bead). The base-labile Fmoc group is used for N-protection. After removing the protecting group (via piperidine hydrolysis) the next amino acid mixture is added using uranium salts as a coupling reagent (for example, TBTU). After the final amino acid is coupled, the N-terminus is acetylated.

The resulting peptides (attached to the polymeric support through its C-terminus) are cleaved with TFA or TFA cleaving cocktails to yield the crude peptide. During this cleavage step, all of the side chains protecting groups are also cleaved. After precipitation with diisopropyl ether, the solid is filtered and dried. The resulting peptides are analyzed and stored at 8° C. or below.

Additionally, any peptide synthesis method that allows synthesis incorporating more than one amino acid species at a controlled ratio in any given position of the peptide sequence is suitable for use with this invention. Further, as described below, DSPs may be peptidomimetics or include unnatural or modified amino acid, necessitating the adaptation to allow addition of such chemical species to the polymers synthesized up to that point.

The synthesis may include unnatural amino acids, or amino acid analogs. In some embodiments, the DSPs are comprised of naturally occurring and synthetic derivatives, for example, selenocysteine. Amino acids further include amino acid analogs. An amino acid “analog” is a chemically related form of the amino acid having a different configuration, for example, an isomer, or a D-configuration rather than an L-configuration, or an organic molecule with the approximate size and shape of the amino acid, or an amino acid with modification to the atoms that are involved in the peptide bond, so as to be protease resistant when polymerized in a polypeptide.

The DSPs for use in the present invention can be composed of L- or D-amino acids or mixtures thereof. As is known by those of skill in the art, L-amino acids occur in most natural proteins. However, D-amino acids are commercially available and can be substituted for some or all of the amino acids used to make DSPs of the present invention. The present invention contemplates DSPs containing both D- and L-amino acids, as well as DSPs consisting essentially of either L- or D-amino acids.

In certain embodiments, the DSPs of the present invention include such linear DSPs that are further modified by substituting or appending different chemical moieties. In one embodiment, such modification is at a residue location and in an amount sufficient to inhibit proteolytic degradation of the DSPs in a subject. For example, the amino acid modification may be the presence in the sequence of at least one proline residue; the residue is present in at least one of carboxy- and amino termini; further, the proline can be present within four residues of at least one of the carboxy- and amino-termini. Further, the amino acid modification may be the presence of a D-amino acid.

In certain embodiments, the subject DSPs is a peptidomimetic. Peptidomimetics are compounds based on, or derived from, peptides and proteins. The DSP peptidomimetics of the present invention typically can be obtained by structural modification of one or more native amino acid residues, e.g., using one or more unnatural amino acids, conformational restraints, isosteric replacement, and the like. The subject peptidomimetics constitute the continuum of structural space between peptides and non-peptide synthetic structures.

Such peptidomimetics can have such attributes as being non-hydrolyzable (e.g., increased stability against proteases or other physiological conditions which degrade the corresponding peptide DSPs), increased specificity and/or potency. For illustrative purposes, peptide analogs of the present invention can be generated using, for example, benzodiazepines (e.g., see Freidinger et al. in “Peptides: Chemistry and Biology,” G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), substituted gamma lactam rings (Garvey et al. in “Peptides: Chemistry and Biology,” G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988, p 123), C-7 mimics (Huffman et al. in “Peptides: Chemistry and Biology,” G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988, p. 105), keto-methylene pseudopeptides (Ewenson et al. J. Med. Chem., 1986, 29:295; and Ewenson et al. in “Peptides: Structure and Function (Proceedings of the 9th American Peptide Symposium),” Pierce Chemical Co. Rockland, Ill., 1985), β-turn dipeptide cores (Nagai et al., Tetrahedron Lett., 1985 26:647; and Sato et al. J. Chem. Soc. Perkin Trans., 1986, 1:1231), β-aminoalcohols (Gordon et al. Biochem. Biophys. Res. Commun., 1985, 126:419; and Dann et al. Biochem. Biophys. Res. Commun., 1986, 134:71), diaminoketones (Natarajan et al. Biochem. Biophys. Res. Commun., 1984, 124:141), and methyleneamino-modified (Roark et al. in “Peptides: Chemistry and Biology,” G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988, p 134). Also, see generally, Session III: Analytic and synthetic methods, in “Peptides: Chemistry and Biology,” G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988.

The molecular weight of a DSP composition can be adjusted during polypeptide synthesis or after the DSPs have been synthesized. To adjust the molecular weight during polypeptide synthesis, the synthetic conditions or the amounts of amino acids are adjusted so that synthesis stops when the polypeptide reaches the approximate length which is desired. After synthesis, polypeptides with the desired molecular weight can be obtained by any available size selection procedure, such as chromatography of the polypeptides on a molecular weight sizing column or gel, and collection of the molecular weight ranges desired. The present polypeptides can also be partially hydrolyzed to remove high molecular weight species, for example, by acid or enzymatic hydrolysis, and then purified to remove the acid or enzymes.

In one embodiment, the DSPs with a desired molecular weight may be prepared by a process which includes reacting a protected polypeptide with hydrobromic acid to form a trifluoroacetyl-polypeptide having the desired molecular weight profile. The reaction is performed for a time and at a temperature which is predetermined by one or more test reactions. During the test reaction, the time and temperature are varied and the molecular weight range of a given batch of test polypeptides is determined. The test conditions which provide the optimal molecular weight range for that batch of polypeptides are used for the batch. Thus, a trifluoroacetyl-polypeptide having the desired molecular weight profile can be produced by a process which includes reacting the protected polypeptide with hydrobromic acid for a time and at a temperature predetermined by test reaction. The trifluoroacetyl-polypeptide with the desired molecular weight profile is then further treated with an aqueous piperidine solution to form a low toxicity polypeptide having the desired molecular weight.

In one particular embodiment, a test sample of protected polypeptide from a given batch is reacted with hydrobromic acid for about 10-50 hours at a temperature of about 20-28° C. The best conditions for that batch are determined by running several test reactions. For example, in one embodiment, the protected polypeptide is reacted with hydrobromic acid for about 17 hours at a temperature of about 26° C.

In certain embodiments, DSP is modified after synthesis. Such modification is useful, for instance, to create DSP to direct the subsequent antibody response to features of the DSP that have application in either a research, diagnostic, or therapeutic context. Examples of post-synthesis modifications include but are not limited to sugars such as glycogen, galactose, glucose, modified sugars such as sialic acid-galactose or its derivatives, (sialic acid=5-amino-3,5-dideoxy-D-glycero-D-galacto-nonulosonic acid) or alternative amino acids such as citrulline. More specific examples of modification by sugars are sialic acid-α2,3-galactose linkage and sialic acid-α2,6-galactose linkage, which is known to affect antigenicity of the epitope. (Suzuki et al, J. Virol. 2000, 74(24): 11825-11831. In one embodiment, the post-synthesis modification is performed using enzymes. In another embodiment, the post-synthesis modification is performed manually using chemical complexation techniques well known in the prior art.

A further embodiment of the instant invention is the use of specific glycosilated/glycogenated forms of a DSP to create antibodies against such a form of a ligand. In one embodiment the ligand itself is a viral coat protein. In another embodiment the ligand itself is an antibody. In one embodiment of the instant invention, the post-translational modification of a DSP is performed using glycogen synthase, or alternatively using chemical complexation techniques well known in the art.

IV. Pharmaceutical Composition

One aspect of the present invention is a pharmaceutical composition comprising a DSP composition. As described below in the method of treatment as an aspect of this invention, the DSP composition produced by the process of the invention is useful in preventing infectious diseases by acting as vaccines.

The DSPs of the present invention may be administered to the subject as a composition which comprises a pharmaceutically effective amount of DSPs and an acceptable carrier and/or excipients. A pharmaceutically acceptable carrier includes any solvents, dispersion media, or coatings that are physiologically compatible. Preferably, the carrier is suitable for oral, rectal, transmucosal (including by inhalation), parenteral, intravenous, intramuscular, intraperitoneal, intradermal, transdermal, topical, or subcutaneous administration. One exemplary pharmaceutically acceptable carrier is physiological saline. Other pharmaceutically acceptable carriers and their formulations are well-known and generally described in, for example, Remington's Pharmaceutical Science (18^(th) Ed., ed. Gennaro, Mack Publishing Co., Easton, Pa., 1990). Various pharmaceutically acceptable excipients are well-known in the art and can be found in, for example, Handbook of Pharmaceutical Excipients (4^(th) ed., Ed. Rowe et al. Pharmaceutical Press, Washington, D.C.). The composition can be formulated as a solution, microemulsion, liposome, capsule, tablet, or other suitable forms. The active component which comprises the copolymer may be coated in a material to protect it from inactivation by the environment prior to reaching the target site of action. The pharmaceutical compositions of the present invention are preferably sterile and non-pyrogenic at the time of delivery, and are preferably stable under the conditions of manufacture and storage. When desirable, the composition further comprises components to enhance stability, permeability, and/or bioavailability, such as particulate forms protective coatings, protease inhibitors or permeation enhancers for various routes of administration, including parenteral, pulmonary, nasal and oral.

For oral administration, the pharmaceutical preparation may be in liquid form, for example, solutions, syrups or suspensions, or may be presented as a drug product for reconstitution with water or other suitable vehicle before use. Such liquid preparations may be prepared by conventional means with pharmaceutically acceptable additives such as suspending agents (e.g., sorbitol syrup, cellulose derivatives or hydrogenated edible fats); emulsifying agents (e.g., lecithin or acacia); non-aqueous vehicles (e.g., almond oil, oily esters, or fractionated vegetable oils); and preservatives (e.g., methyl or propyl-p-hydroxybenzoates or sorbic acid). The pharmaceutical compositions may take the form of, for example, tablets or capsules prepared by conventional means with pharmaceutically acceptable excipients such as binding agents (e.g., pre-gelatinized maize starch, polyvinyl pyrrolidone or hydroxypropyl methylcellulose); fillers (e.g., lactose, microcrystalline cellulose or calcium hydrogen phosphate); lubricants (e.g., magnesium stearate, talc or silica); disintegrants (e.g., potato starch or sodium starch glycolate); or wetting agents (e.g., sodium lauryl sulfate). The tablets may be coated by methods well-known in the art.

In one embodiment, the oral composition is enterically-coated. Use of enteric coatings is well known in the art. For example, Lehman (1971) teaches enteric coatings such as Eudragit S and Eudragit L. The Handbook of Pharmaceutical Excipients, 2^(nd) Ed., also teaches Eudragit S and Eudragit L applications. One Eudragit which may be used in the present invention is L30D55. Preparations for oral administration may be suitably formulated to give controlled release of the active compound.

The compositions may also be formulated in rectal compositions such as suppositories or retention enemas, e.g., containing conventional suppository bases such as cocoa butter or other glycerides.

For administration by inhalation, the compositions for use according to the present invention are conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebulizer, with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of, e.g., gelatin, for use in an inhaler or insufflator may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch.

The compositions may be formulated for administration by injection, e.g., by bolus injection or continuous infusion in a parenteral, intravenous, intraperitoneal, intramuscular, or subcutaneous manner. Formulations for injection may be presented in unit dosage form, e.g., in ampoules or in multi-dose containers, with an added preservative. The compositions may take such forms as suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents. Alternatively, the active ingredient may be in powder form for reconstitution with a suitable vehicle, e.g., sterile pyrogen free water, before use.

In a preferred embodiment, compositions comprising DSP compositions are formulated in accordance with routine procedures as pharmaceutical compositions adapted for intravenous administration to human beings. Typically, compositions for intravenous administration are solutions in sterile isotonic aqueous buffer. Where necessary, the composition may also include a solubilizing agent and a local anesthetic such as lignocaine to ease pain at the site of the injection. Generally, the ingredients are supplied either separately or mixed together. Where the composition is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline, with the intervals between administrations being greater than 24 hours, 32 hours, or more preferably greater than 36 or 48 hours. Where the composition is administered by injection, an ampoule of sterile water or saline for injection can be provided so that the ingredients may be mixed prior to administration.

In other embodiments of the present invention, the pharmaceutical compositions are regulated-release or sustained release formulations. DSP compositions of the present invention may be admixed with biologically compatible polymers or matrices which control the release rate of the copolymers into the immediate environment. Controlled or sustained release compositions include formulation in lipophilic depots (e.g., fatty acids, waxes, oils). One embodiment of sustained release formulations is transdermal patches.

In some embodiments of the present invention, pharmaceutical compositions comprise DSPs formulated with oil and emulsifier to form water-in-oil microparticles and/or emulsions. The oil may be any non-toxic hydrophobic material liquid at ambient temperature to about body temperature, such as edible vegetable oils including safflower oil, soybean oil, corn oil, and canola oil; or mineral oil. Chemically defined oil substance such as lauryl glycol may also be used. The emulsifier useful for this embodiment includes Span 20 (sorbitan monolaurate) and phosphatidylcholine. In some embodiments, a DSP composition is prepared as an aqueous solution and is prepared into an water-in-oil emulsion dispersed in 95 to 65% oil such as mineral oil, and 5 to 35% emulsifier such as Span 20. In another embodiment of the invention, the emulsion is formed with alum rather than with oil and emulsifier. These emulsions and microparticles reduce the speed of uptake of DSPs, and achieve controlled delivery.

In another embodiment, the controlled and/or sustained delivery is achieved by implantable medical devices coated with sustained-release formulations, or implantable pharmaceutical formulation suitable for sustained-release of the active components.

In some embodiments of the invention, pharmaceutical compositions comprise a set of nucleic acid vectors encoding a DSP composition, which is expressed as polypeptides within a subject. The vectors may comprise transcription- and/or translation-controlling elements such that the timing and level of the DSPs composition produced may be regulated.

In some embodiments, the vectors also comprise one or more additional coding sequences, which encodes a therapeutically beneficial polypeptide or a second, different composition of DSPs that is not a member of the first DSP composition. In alternative embodiments, a pharmaceutical composition comprises one or more vectors, each encoding either: the DNA sequences for the DSPs of a first DSP composition, or the DNA sequences for the DSPs of a second DSPs composition or a therapeutically beneficial polypeptide, that is not a member of the first DSP composition. Such therapeutically beneficial polypeptide may be, for example, an immunomodulatory cytokine or a growth factor.

Some embodiments of the invention are pharmaceutical compositions for targeted delivery of the DSP composition of the invention. In such embodiments, a pharmaceutical composition comprises a DSP composition that is complexed with a targeting moiety. The targeting moiety allows localized delivery of the DSP composition to a desired location or microenvironment within the subject. A targeting moiety include, and may be selected from, the group comprising a chemical group or functionality such as biotin or simple sugars, a single or double stranded DNA sequence of various lengths, a single or double stranded RNA sequence of various lengths, a peptide of various lengths, an antibody including single chain antibodies, Fab′, or modified antibodies, a lipid, or a glycolipid. More than one of such moiety may be used at the same time in combination. For examples of targeting moieties, see U.S. Pat. No. 6,268,488; U.S. Appl. Pub. No. 2003/0190676; and see, for example, www.covx.com/tech_creating.html.

In one embodiment of the invention, the complex has characteristics of a prodrug, causing the DSP composition to exhibit no pharmaceutical activity of the present invention until the dissolution of the complex in the subject. In another embodiment, the complex does not affect the activity of the DSP composition.

Any methods generally known to one skilled in the art may be used to produce a complex of the instant invention and a targeting moiety. The target moiety may be complexed to the DSPs by a chemical bond, which may be covalent, ionic, hydrophobic, or van der Waals force, directly or through another chemical entity. Alternatively, the target moiety may be co-localized with the DSPs through common medium such as a biocompatible resin within which the DSP composition is included. The manner of forming a complex is chosen also based on the active state of the instant invention while existing in the combination and whether a permanent complex or a transitory complex is desired.

In some embodiments, the pharmaceutical compositions also include additional therapeutically active agents. Such additional ingredient can be one or more of: an additional DSP composition that binds to a different target, an antibody which activates inflammatory molecules, or cytokines. Further additional ingredient can be activating cytokines and chemokines (as described in Shaw, Jennifer, Infection and Immunity 2001, 69:4667-4672) taken from the group consisting of Mip1β, Mip1α, Mip-2, Mip3α, IP-10, MCP-1, TCA-3, IL-1, IL-18, IL-6, IFNγ, MIF, IL-12, CCR7.

Further, a form of vitamin D that is or becomes biologically active within the body of the subject receiving such form of vitamin D may also be used as an additional ingredient. The two main forms of vitamin D are: vitamin D3 or cholecalciferol, which is formed in the skin after exposure to sunlight or ultraviolet light, and ergocalciferol or vitamin D2 which is obtained by irradiation of plants or plant materials or foods. The differences are situated in the side chain. Vitamin D3 may be obtained from natural sources such as fatty fish such as herring and mackerel. In the body, two other forms of vitamin D3 can be found. Vitamin D3 is hydroxylated in the liver into 25-hydroxyvitamin D3 (25(OH)D), and subsequently in the kidney into 1,25-dihydroxyvitamin D3 (1,25(OH)2D), which is the active metabolite that stimulates the calcium absorption from the gut (Feldman et al., 2005). When 1,25(OH)2D is sufficiently available, 24,25-dihydroxyvitamin D (24,25(OH)2D) is formed in the kidney, which is further catabolized.

Another class of therapeutically active agents useful as an additional agent is immune boosters which increases the production of common lymphoid precursors (CLPs) from the multilineage potential cells. An example of such agent is PBI-1402 developed by ProMetic in Quebec, Canada.

The invention further provides a kit comprising (i) a composition comprising a DSP composition or DNA delivery vehicle comprising DNA encoding DSPs and (ii) instructions for administering the composition to a subject in need thereof at intervals greater than 24 hours, more preferably greater than 36 hours, for the treatment of a disease, such as an infection with an invading pathogen. In one embodiment, the invading pathogen is a virus. In a preferred embodiment, the virus is influenza. In a preferred embodiment, the DSP composition is formulated in dosages for administration of greater than about 24, 30, 36, 42, 48, 54, 60, 66, 72, 78, 84, 90, 96, 102, 108, 114, 120, 126, 132, 138, 144, 150, 156, 162, 168, 174, 180, 186, 192, 198, 204, 210, 216, 222, 228, 234, or 240 hours, or any intervening interval thereof. In another embodiment of the kits described herein, the instructions indicate that the DSP is to be administered every about 24, 30, 36, 42, 48, 54, 60, 66, 72, 78, 84, 90, 96, 102, 108, 114, 120, 126, 132, 138, 144, 150, 156, 162, 168, 174, 180, 186, 192, 198, 204, 210, 216, 222, 228, 234, or 240 hours, or any interval in between. Kits may comprise additional components, such as packaging, instructions, and one or more apparatuses for the administration of the copolymer, such as a hypodermic syringe

V. Methods of Treatment

The instant invention provides for a further improvement on the need to improve the effectiveness of vaccines. The improvement takes form in an ability to dynamically administer the compound based on the ability of the compound to achieve an increased immune activation, while generating either a T_(H)1 immune posture, or a T_(H)2 immune posture, and while producing anti-compound antibodies at either a low or a high level. Dynamic administration of random sequence copolymer is comprised of any combination of dose, regimen, route of administration, and/or formulation. This dynamic immunomodulation provides for increased effectiveness at any of the multiple stages of a disease within a particular patient, as well as the ability to treat multiple, pathogenic antigenic-determinant unrelated diseases more effectively.

The invention provides methods for the treatment of a disease or prevention of further progression of a disease (including a disease in its latent stage) in a subject, preferably in a human, which subject is afflicted with or is suspected to be afflicted with the disease. Another embodiment of the present invention is a method for prophylactically treating a subject at risk of developing e.g., an infectious disease by administering a DSP composition. A subject at risk is identified by, for example, determining the genetic susceptibility to an infectious disease by testing for alleles of HLA, and/or based on familial history, geographic location, economic or social situations, or genetic markers.

A particular aspect of the invention is a method of protecting a subject from an influenza infection wherein the influenza virus is a new immunologic subtype comprising the step of administering a pharmaceutical composition comprising a DSP composition the base sequence of which comprises an epitope from hemagglutinin of an influenza virus subtype that caused the most immediate past epidemic at any given time when such protection is desired. Such new subtype may occur either by antigenic drift or antigenic shift. By the most immediate past epidemic, it is meant that, at any given time when such protection is desired, there would have been the last infectious event that infected a large number of people. The DSPs of the invention that would be created using the region of HA from such most immediate past epidemic, which region corresponds to SEQ ID NO: 6 or 7 and contains epitopes, are expected to be particularly effective in conferring immunity to the next flu surge, whether it is a simple antigenic drift or it is a major antigenic shift. This is because there is immunological overlap between two temporally adjacent flu epidemics, and expansion of immunoloreactivity that the DSPs induces can be expected to confer adequate protection to a new influenza subtype that would otherwise be recognized as a new and unknown antigen.

One aspect of the invention provides methods of treating or preventing a disease, the method comprising administering to said subject a dosing regimen of an effective amount of a DSP composition for the protection against infection by an invading pathogen treatable with the DSP composition, said effective amount delivered to said subject once, twice, or multiple times at time intervals greater than 24 hours, 36 hours, or more preferably greater than 48 hours. A DSP composition may be administered more than once as a booster dose. A related aspect of the invention provides a method for the treatment of a subject in need thereof, comprising administering to said subject a dosing regimen of an effective amount of a DSP composition for the amelioration of a disease treatable with the DSP composition, said effective amount delivered to the subject using a sustained-release formulation which administers the DSP composition over a period of at least 2 days, at least 4 days, or at least 6 days, or at least 10 days, or at least 14 days, or at least 28 days, wherein the effective amount is an amount that is effective if delivered daily.

One aspect of the invention is the administration of a DSP composition to a subject in need thereof, as described above, in combination with other therapeutic agents that are effective in treating the conditions that are treated by administration of the DSP, or conditions that accompany or occur concurrently with the conditions that are treated by administration of the DSP. The additional therapeutically active agents may treat the same or related disease as the DSP composition, or may be intended to treat an undesirable side effect of administration of the DSP composition, such as to reduce swelling at a site of intradermal injection. Alternatively, the other therapeutic agents enhance the activity of DSP compositions. Such additional therapeutic agents are, by way of example, antibodies, cytokines, growth factors, enzyme inhibitors, antibiotics, antiviral agents, anti-inflammatory including steroids, immune boosters, antimetabolites, soluble cytokine receptors, and vitamin D or agents that increase the level of circulating vitamin D, toll-like receptor agonists, CpG oligodeoxynucleotides, surface charged poly(lactide-co-glycolide) microparticles, any of the above encapsulated into liposomes, archaeosome adjuvants, mucosal adjuvants, polyphosphazenes. Adjuvants may include aluminium hydroxide, aluminium phosphate and calcium phosphate, other adjuvants based on oil emulsions, products from bacteria (their synthetic derivatives as well as liposomes) or non-infectious gram-negative bacteria, endotoxins, cholesterol, fatty acids, aliphatic amines, paraffinic and vegetable oils, monophosphoryl lipid A, ISCOMs with Quil-A, and Syntex adjuvant formulations (SAFs) containing the threonyl derivative or muramyl dipeptide, or toll-like receptor antagonists or agonists. Additional therapeutically active agents also include copolymers which bind to a HLA molecule associated with the disease such as Copolymer-1, or another DSP composition. The HLA molecule may be an HLA-DQ molecule or an HLA-DR molecule. The enzyme inhibitor may be a protease inhibitor or a cyclooxygenase inhibitor. Examples of the therapeutically active agents to be administered in conjunction with the DSP composition are recited in Section IV, “Pharmaceutical Composition” section, though the administration of these agents are not limited to co-administration as a single composition. The additional therapeutic agents may be administered before, concomitantly with, or after the administration of the DSP composition, at such time that the effect of the additional therapeutic agents and the effect of the DSP composition overlap at some time point.

In one embodiment of the methods described herein, the route of administration can be oral, intraperitoneal, transdermal, subcutaneous, by intravenous or intramuscular injection, by inhalation, topical, intralesional, or by infusion; liposome-mediated delivery; buccal, intrathecal, gingival pocket, rectal, intravaginal, intrabronchial, nasal, transmucosal, intestinal, ocular or otic delivery, or any other methods known in the art as one skilled in the art may easily perceive. Administration can be systemic or local. In the event more than one DSP composition is being administered to a subject during the same or overlapping time period, such additional therapeutic agent may be administered by a route different from that for the administration of the DSP composition.

In general, an embodiment of the invention is a method of administering a suitable dose of a therapeutic DSP composition that will be the lowest effective dose to produce a therapeutic effect, for example, mitigating symptoms. The therapeutic DSP compositions are preferably administered at a dose per subject, which corresponds to a dose per day of at least about 0.0001 mg, at least about 0.002 mg, at least about 0.02 mg, at least about 0.2 mg, at least about 2 mg, or at least about 10 mg as appropriate minimal starting dosages, or about x mg, wherein x is one thousandth of an integer between 1 and 20. In one embodiment of the methods described herein, a dose of about 0.0001 to about 500 mg/kg, can be administered. In general, the effective dosage of the DSP composition of the present invention is from about 0.050 to about 400 micrograms of the composition per kilogram (i.e. 0.00005 to 0.4 mg/kg) of the subject per day, and more specifically, 0.001 to 0.01 mg/kg of the subject per day. In one specific embodiment, the equivalent dosage per day, regardless of the frequency with which the doses are administered, is from about 0.05 to 100, or more specifically, from about 0.10 to 40, or from about 1 to 20, or more specifically about 2.0 mg/day. In another specific embodiment, each individual dosage in the treatment regimen is from about 0.0001 to 100 mg, more specifically a dose of about 0.001 to 1 mg, more specifically a dose of about 0.001 to 0.01 mg per dose. In certain embodiments, total dosage per day is and total dose per day. In another specific embodiment, the dosage is determined in relation to the body surface area of a subject. In general, the effective dosage of the DSP composition is from about 0.05 to 100 microgram/m², more specifically from about 0.10 to 50, or more specifically from about 0.38 to 38 microgram/m² of the body surface area of a subject.

However, it is understood by one skilled in the art that the dose of the DSP composition of the invention will vary depending on the subject and upon the particular route of administration used. It is routine in the art to adjust the dosage to suit the individual subjects. Additionally, the effective amount may be based upon, among other things, the size of the DSPs, the biodegradability of the DSPs, the bioactivity of the DSPs and the bioavailability of the DSPs. If the DSPs does not degrade quickly, such as is expected when the DSPs comprise unnatural amino acids or are peptidomimetics, is bioavailable and highly active, a smaller amount will be required to be effective. The actual dosage suitable for a subject can easily be determined as a routine practice by one skilled in the art, for example a physician or a veterinarian given a general starting point. For example, the physician or veterinarian could start doses of the DSP composition of the invention employed in the pharmaceutical composition at a level lower than that required in order to achieve the desired therapeutic effect, and increase the dosage with time until the desired effect is achieved. The dosage of the DSP composition may either be increased in the event the patient does not respond significantly to current dosage levels, or the dose may be decreased if an alleviation of the symptoms of the disorder or disease state is observed, or if the disorder or disease state has been ablated, or if an unacceptable side effects are seen with the starting dosage.

In one embodiment, a therapeutically effective amount of the DSP composition is administered to the subject in a treatment regimen comprising intervals of at least 36 hours, or more preferably 48 hours, between dosages. In another embodiment, the DSP composition is administered at intervals of at least 54, 60, 66, 72, 78, 84, 90, 96, 102, 108, 114, 120, 126, 132, 138, 144, 150, 156, 162, 168, 174, 180, 186, 192, 198, 204, 210, 216, 222, 228, 234, or 240 hours, or the equivalent amount of days. In some embodiments, the DSP composition is administered every other day, while in other embodiments it is administered weekly. If two different DSP compositions, or DSP composition with another therapeutic agent, are administered to the subject, such administration may take place at the same time, such as simultaneously, or essentially at the same time, such as in succession. Alternatively, their administration may be staggered. For example, two DSP compositions which are each administered every 48 hours may both be administered on the same days, or one may be administered one day and the other on the next day and so on in an alternating fashion.

In other embodiments, the DSP composition is administered in a treatment regimen which comprises at least one uneven time interval, wherein at least one of the time intervals is at least 24, 30, 36, 42, 48, 54, 60, 66, 72, 78, 84, 90, 96, 102, 108, 114, 120, 126, 132, 138, 144, 150, 156, 162, 168, 174, 180, 186, 192, 198, 204, 210, 216, 222, 228, 234, or 240 hours, or the equivalent amount of days.

In one embodiment, the DSP composition is administered to the subject once. In one embodiment, the DSP composition is administered to the subject at least twice during a treatment regimen. Accordingly, in one embodiment, at least one of the time intervals between administrations is greater than about 24, 30, 36, 42, 48, 54, 60, 66, 72, 78, 84, 90, 96, 102, 108, 114, 120, 126, 132, 138, 144, 150, 156, 162, 168, 174, 180, 186, 192, 198, 204, 210, 216, 222, 228, 234, or 240 hours.

In another embodiment, the dosage regimen consists of two or more different interval sets. For example, a first part of the dosage regimen is administered to a subject daily, every other day, or every third day, for example, at about 22 mg copolymer/m² body surface area of the subject, wherein the subject is a human. In some embodiment of the invention, the dosing regimen starts with dosing the subject every other day, every third day, weekly, biweekly, or monthly. The dosage for administration every other day or every third day may be up to about 65 mg/m² and 110 mg/m² respectively. For a dosing regimen comprising dosing of the random copolymer every week, the dose comprises up to about 500 mg/m², and for a dosing regimen comprising dosing of the random copolymer every two weeks or every month, up to 1.5 g/m² may be administered. The first part of the dosing regimen may be administered for up to 30 days, for example, 7, 14, 21, or 30 days. A subsequent second part of the dosing regimen with a different, longer interval administration with usually lower exposure (step-down dosage), administered weekly, every 14 days, or monthly may optionally follow, for example, at 500 mg/m² body surface area weekly, up to maximum of about 1.5 g/m² body surface area, continuing for 4 weeks up to two years, for example, 4, 6, 8, 12, 16, 26, 32, 40, 52, 63, 68, 78, or 104 weeks. Alternatively, if the disease goes into remission or generally improves, the dosage may be maintained or kept at lower than maximum amount, for example, at 140 mg/m² body surface area weekly. If, during the step-down dosage regimen, the disease condition relapses, the first dosage regimen may be resumed until effect is seen, and the second dosing regimen may be implemented. This cycle may be repeated multiple times as necessary.

In other embodiments of the invention, any of the methods of the invention may be practiced using sustained release formulation comprising a DSP composition. When administering a DSP composition of the invention using a sustained release formula, the overall exposure to the DSP is generally lower than in bolus administration. For example, a first part of the dosage regimen is administered to a subject daily, every other day, or every third day, for example, at about 22 mg DSP/m² body surface area of the subject per dose, wherein the subject is a human. In some embodiment of the invention, the dosing regimen uses sustained release formula, dosing the subject every other day, every third day, weekly, biweekly, or monthly so that the copolymer is released during the interval. The dosage for administration every other day or every third day may be up to about 35 mg/m² and 65 mg/m² per dose, respectively. For a dosing regimen comprising dosing of the DSP composition every week, the dose comprises up to about 140 mg/m² per dose, and for a dosing regimen comprising dosing of the DSP composition every two weeks or every month, up to 750 mg/m² may be administered. The first part of the dosing regimen may be administered for up to 30 days, for example, 7, 14, 21, or 30 days. A subsequent second part of the dosing regimen with a different, longer interval administration with usually lower exposure (step-down dosage), administered weekly, every 14 days, or monthly may optionally follow, for example, at 140 mg/m² body surface area weekly, up to maximum of about 1.5 g/m² body surface area, continuing for 4 weeks up to two years, for example, 4, 6, 8, 12, 16, 26, 32, 40, 52, 63, 68, 78, or 104 weeks. Alternatively, if the disease goes into remission or generally improves, the dosage may be maintained or kept at lower than maximum amount, for example, at 140 mg/m² body surface area weekly. If, during the step-down dosage regimen, the disease condition relapses, the first dosage regimen may be resumed until effect is seen, and the second dosing regimen may be implemented. This cycle may be repeated multiple times as necessary.

For such sustained release administration, such method comprises applying a sustained-release transdermal patch or implanting a sustained-release capsule or a coated implantable medical device so that a therapeutically effective dose of the copolymer of the present invention is delivered at defined time intervals to a subject of such a method. The DSP composition of the subject invention may be delivered via a capsule which allows regulated-release of the DSPs over a period of time. Controlled or sustained-release compositions include formulation in lipophilic depots (e.g., fatty acids, waxes, oils). Also comprehended by the invention are particulate compositions coated with polymers (e.g., poloxamers or poloxamines). In certain embodiments, a source of a DSP composition is stereotactically provided within or proximate to the area of pathogenic attack.

An improvement in the symptoms of a subject afflicted with a disease as a result of administration of the DSP composition may be noted by a decrease in frequency of recurrences of episodes of the disease symptoms, by decrease in severity of symptoms, and by elimination of recurrent episodes for a period of time after the start of administration. A therapeutically effective dosage preferably reduces symptoms and frequency of recurrences by at least about 20%, for example, by at least about 40%, by at least about 60%, and by at least about 80%, or by about 100% elimination of one or more symptoms, or elimination of recurrences of the autoimmune disease, relative to untreated subjects. The period of time can be at least about one month, at least about six months, or at least about one year.

DEFINITIONS

The term “associated with” means “coexistent with” or “in correlation with.” The term does not necessarily indicate causal relationship, though such relationship may exist.

The term “binding” refers to a direct association between two molecules, due to, for example, covalent, electrostatic, hydrophobic, ionic and/or hydrogen-bond interactions under physiological conditions, and including interactions such as salt bridges and water bridges.

The term “HLA molecule” means any class II major histocompatibility complex glycoproteins.

The term “immunomodulation” means the process of increasing or decreasing the immune system's ability to mount a response against a particular antigenic determinant through the T-cell receptor (“TCR”)'s recognition of complexes formed by major histocompatibility complex (“MHC”) and antigens.

The term “patient” refers to an animal, preferably a mammal, including humans as well as livestock and other veterinary subjects.

The terms “peptide”, “polypeptide” and “protein” are used interchangeably herein. These terms refer to unmodified amino acid chains, and also include minor modifications, such as phosphorylations, glycosylations and lipid modifications. The terms “peptide” and “peptidomimetic” are not mutually exclusive and include substantial overlap.

A “peptidomimetic” includes any modified form of an amino acid chain, such as a phosphorylation, capping, fatty acid modification and including unnatural backbone and/or side chain structures. As described below, a peptidomimetic comprises the structural continuum between an amino acid chain and a non-peptide small molecule. Peptidomimetics generally retain a recognizable peptide-like polymer unit structure. Thus, a peptidomimetic may retain the function of binding to a HLA protein forming a complex which activates autoreactive T cells in a patient suffering from an autoimmune disease.

The term “amino acid residue” is known in the art. In general the abbreviations used herein for designating the amino acids and the protective groups are based on recommendations of the IUPAC-IUB Commission on Biochemical Nomenclature (see Biochemistry (1972) 11:1726-1732). In certain embodiments, the amino acids used in the application of this invention are those naturally occurring amino acids found in proteins, or the naturally occurring anabolic or catabolic products of such amino acids which contain amino and carboxyl groups. Particularly suitable amino acid side chains include side chains selected from those of the following amino acids: glycine, alanine, valine, cysteine, leucine, isoleucine, serine, threonine, methionine, glutamic acid, aspartic acid, glutamine, asparagine, lysine, arginine, proline, histidine, phenylalanine, tyrosine, and tryptophan.

The term “amino acid residue” further includes analogs, derivatives and congeners of any specific amino acid referred to herein, as well as C-terminal or N-terminal protected amino acid derivatives (e.g. modified with an N-terminal or C-terminal protecting group). For example, the present invention contemplates the use of amino acid analogs wherein a side chain is lengthened or shortened while still providing a carboxyl, amino or other reactive precursor functional group for cyclization, as well as amino acid analogs having variant side chains with appropriate functional groups). For instance, the subject compound can include an amino acid analog such as, for example, cyanoalanine, canavanine, djenkolic acid, norleucine, 3-phosphoserine, homoserine, dihydroxy-phenylalanine, 5-hydroxytryptophan, 1-methylhistidine, 3-methylhistidine, diaminopimelic acid, ornithine, or diaminobutyric acid. Other naturally occurring amino acid metabolites or precursors having side chains which are suitable herein will be recognized by those skilled in the art and are included in the scope of the present invention.

Most of the amino acids used in the DSPs of the present invention may exist in particular geometric or stereoisomeric forms. In preferred embodiments, the amino acids used to form the subject DSPs are (L)-isomers, although (D)-isomers may be included in the DSPs such as at non-anchor positions or in the case of peptidomimetic versions of the DSPs.

“Prevent”, as used herein, means to measurably delay or preclude the onset of, for example, one or more symptoms, of a disorder or condition.

“Treat”, as used herein, means at least lessening the severity or ameliorating the effects of, for example, one or more symptoms, of a disorder or condition.

“Treatment regimen” as used herein, encompasses therapeutic, palliative and prophylactic modalities of administration of one or more compositions comprising one or more DSP compositions. A particular treatment regimen may last for a period of time at a particular dosing pattern, which will vary depending upon the nature of the particular disease or disorder, its severity and the overall condition of the patient, and may extend from once daily, or more preferably once every 36 hours or 48 hours or longer, to once every month or several months.

The practice of the present invention will employ, where appropriate and unless otherwise indicated, conventional techniques of cell biology, cell culture, molecular biology, transgenic biology, microbiology, virology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are described in the literature. See, for example, Molecular Cloning: A Laboratory Manual, 3rd Ed., ed. by Sambrook and Russell (Cold Spring Harbor Laboratory Press: 2001); the treatise, Methods In Enzymology (Academic Press, Inc., N.Y.); Using Antibodies, Second Edition by Harlow and Lane, Cold Spring Harbor Press, New York, 1999; Current Protocols in Cell Biology, ed. by Bonifacino, Dasso, Lippincott-Schwartz, Harford, and Yamada, John Wiley and Sons, Inc., New York, 1999; and PCR Protocols, ed. by Bartlett et al., Humana Press, 2003; PHARMACOLOGY A Pathophysiologic Approach Edited by Josehp T. DiPiro, Robert Talbert, Gary, Yee, Gary Matzke, Barbara Wells, and L. Michael Posey. 5th edition 2002 McGraw Hill; Pathologic Basis of Disease. Ramzi Cotran, Vinay Kumar, Tucker Collins. 6th Edition 1999. Saunders.

Example 1 Preparation of a DSP Composition from Fictitious Base Peptides

For ease of understanding, as an illustration, preparation of a DSP composition deriving from two fictitious peptide sequences, representing a known epitope, is described and shown in the table depicted in FIG. 6. In this illustration, the cassettes consist of five amino acids each, (×1, ×2, ×3, ×4, ×5=THMCE in y₁ and PWKNA in y₂). THMCE is defined as having an input ratio of a=7, b=1, c=1, d=1, e=10. PWKNA is defined as having an input ratio of a=1, b=3, c=3, d=3, e=20. For synthesis, the identity of group of amino acids occupying each amino acid position for each peptide is determined using the preferred method of amino acid substitution described by Kosiol et al., J. Theoretical Biol. 228:97-106, 2004, as shown in FIG. 4 (or less preferably an equivalent means of systematically altering amino acids), and the overall ratio of amino acids that occupy each of such positions in the resulting collective DSP composition is given above. Each cassette, y₁ and y₂, will twice be repeated two times, generating an order of y₁ y₁ y₂ y₂ y₁ y₁ y₂ y₂. N_(n) are the number of times the sequence within the cassette is to be repeated, and in our fictitious example N=2. MN can be any type of modifying moiety. MN must be amenable to solid phase synthesis methods. For this fictitious example, a modifying moiety of amino acids that would target the DSP to a certain location within a subject is chosen, such as an RGD-based sequence motif on a particular integrin such as alphaVbeta3. In this example the C-terminal modifier will also be an RGD-based motif, but comprised of D-amino acids.

The DSP composition as described above is prepared using a solid phase peptide synthesis method as described elsewhere in this disclosure.

Example 2 Preparation of a DSP Composition from Influenza Hemagglutinin Epitope as a Source Peptide

As a starting point, a hemagglutinin sequence of a strain of influenza A subtype H5N1 avian flu virus isolated from an infected human, A/Egret/Egypt/1162/NAMRU-3/06, is chosen (Steven J et al., J Mol Biol, 2008 381:1382-94). The ascension number, ACD62257, and sequence, SEQ ID No: 15, is found using the database: http://www.ncbi.nlm.nih.gov/genomes/FLU/Database/multiple.cgi. A 3D protein structure is created using RasMol (http://rasmol.org/), or an equivalent, after obtaining a model using ModBase (Nucleic Acids Research 34, D291-D295, 2006), or an equivalent comparative modeling database. A BLAST search is performed, (http://www.ncbi.nlm.nih.gov/sutils/blast_table.cgi?taxid=11308&selectall), using the advanced BLAST to retrieve a maximum number of sequences, in order to identify homologous influenza A, B, or C variants. A phylogenic tree is created using fast minimum evolution, 0.85 maximum sequence Grishin difference. The leading node in the tree is selected to obtain an alignment of the entire tree. The alignment is analyzed for mutations in amino acids between the different flu variants obtained in the search in order to obtain rules for amino acid substitution. A summary of the mutations is made in order to determine the pattern and frequency of mutations at each amino acid position. The mutation patterns are coded into RasMol so that the identification of variable regions in the context of the 3D structure of the viral protein. The ACD62257 HA aa 115-163 sequence is shown below as row 1. Based on the variant identification, analysis and summary, amino acids are chosen and placed into rows 2 through 6, with row 7 always being Alanine. An exemplary percentage of how to mix these amino acids in a peptide synthesis procedure is shown in the subsequent rows. The methods and rules to define the identity of amino acids for each position of the resulting peptides are described above in Example 1. As with Example 1, the DSP composition is synthesized using a solid phase peptide synthesis method.

Position 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 Amino Acids 1 C I I P K S S W S D H E A S S G V 2 P S D L 3 N 4 5 6 7 A A A A A A A A A A A A A Percentage 1 100 70 70 70 70 70 70 70 70 40 90 65 100 90 65 100 100 2 20 20 25 25 3 30 4 5 6 7 30 30 30 30 30 30 30 10 10 10 10 10 10 TOTAL 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 Position 18 19 20 21 22 23 24 25 26 27 23 29 30 31 32 33 34 Amino Acids 1 S S A C P Y Q G R S S F F R N V V 2 A H K P Y 3 N S 4 L V 5 T 6 G 7 A A A A A Percentage 1 100 100 100 100 100 40 90 20 45 100 100 100 100 100 100 100 2 30 15 45 3 20 15 4 15 5 15 6 10 7 100 10 10 10 10 TOTAL 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 Position 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 Amino Acids 1 W L I K K D N A Y P T I K R S Y C 2 T T R N S T K 3 V E D S 4 5 6 7 A A A A A Percentage 1 100 100 70 70 80 45 40 40 100 100 100 100 100 60 100 100 100 2 10 10 10 45 40 40 40 3 10 10 10 20 4 5 6 7 10 10 10 10 10 TOTAL 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 Once formulated into a pharmaceutically acceptable preparation, the DSP is administered to a subject in need of immune protection against the drift-variants associated with the A/Egret/Egypt/1162/NAMRU-3/06 cluster. The DSP directs the subject's immune response to all of the variants within the cluster, thus anticipating multiple directions the transition, or shift, from one cluster to another more virulent cluster will take (Smith D J et al., Science 305:371-6, 2004), Once the new dominant shifted variants are identified through the Global Surveillance network, or equivalent, a new H5N1 HA-based DSP polymer is designed, manufactured and administered using the above methods.

It can be easily discerned by one skilled in the art that the above example is repeatable with subsequent strains of H5N1, with other serological variants or with other viral proteins selected from the group consisting of CMV glycoproteins B, H, and gCIII, HIV-1 envelope, glycoproteins, RSV envelope glycoproteins, HSV envelope glycoproteins, EBV envelope glycoproteins, VZV envelope glycoproteins, HPV envelope glycoproteins, Hepatitis family surface antigens

The following references are exemplary sources of epitopes useful as base peptide sequences

-   Diamond, D. et al., Blood 90:1751-57 (1997) 1 -   Belyakov, I., Proc. Nat. Acad. Sci. USA, 95:1709 (1998) 2 -   Saad, M. D., et al., direct submission to GenBank, ACD62257 3 Viral     and Zoonotic Diseases Research Program, U.S. Naval Medical Research     Unit No. 3, Extension of Ramses Street, Nasr City, Cairo 11517,     Egypt -   Mase, M., et al., “Characterization of H5N1 influenza A viruses 4     isolated during the 2003-2004 influenza outbreaks in Japan”,     Virology 332 (1), 167-176 (2005) -   Kaverin, N. V. et al., “Structure of antigenic sites on the 5     hemagglutinin molecule of H5 avian influenza virus and phenotypic     variation of escape mutants,” J. Gen. Virol. 83: 2497-2505 (2002)

The contents of any patents, patent applications, patent publications, or scientific articles referenced anywhere in this application are herein incorporated in their entirety.

Sequence Listings in Addition to Table I

HEMAGGLUTININ INFLUENZA A VIRUS (A/BRISBANE/59/2007(H1N1)) ACCESSION CA28844 SEQ ID NO: 8 MKVKLLVLLC TFTATYADTI CIGYHANNST DTVDTVLEKN VTVTHSVNLL ENSHNGKLCL LKGIAPLQLG NCSVAGWILG NPECELLISK ESWSYIVEKP NPENGTCYPG HFADYEELRE QLSSVSSFER FEIFPKESSW PNHTVTGVSA SCSHNGESSF YRNLLWLTGK NGLYPNLSKS YANNKEKEVL VLWGVHHPPN IGDQKALYHT ENAYVSVVSS HYSRKFTPEI AKRPKVRDQE GRINYYWTLL EPGDTIIFEA NGNLIAPRYA FALSRGFGSG IINSNAPMDK CDAKCQTPQG AINSSLPFQN VHPVTIGECP KYVRSAKLRM VTGLRNIPSI QSRGLFGAIA GFIEGGWTGM VDGWYGYHHQ NEQGSGYAAD QKSTQNAING ITNKVNSVIE KMNTQFTAVG KEFNKLERRM ENLNKKVDDG FIDIWTYNAE LLVLLENERT LDFHDSNVKN LYEKVKSQLK NNAKEIGNGC FEFYHKCNDE CMESVKNGTY DYPKYSEESK LNREKIDGVK LESMGVYQIL AIYSTVASSL VLLVSLGAIS FWMCSNGSLQ CRICI HEMAGGLUTININ [INFLUENZA A VIRUS (A/SOUTH AUSTRALIA/55/2005(H1N1) ACCESSION ABJ16653 SEQ ID NO: 9 MKVKLLVLLC TFTATYADTI CIGYHANNST DTVDTVLEKN VTVTHSVNLL EGSHNGKLCL LKGIAPLQLG NCSVAGWILG NPECELLISK ESWSYIVETP NPENGTCYPG YFADYEELRE QLSSVSSFER FEIFPKESSW PNHTVTGVSA SCSHNGKSSF YRNLLWLTGK NGLYPNLSKS YANNKEKEVL VLWGVHHPPN IGBQRALYHT ENAYVSVVSS HYSRRFTPEI AKRPKVRDQE GRINYYWTLL EPGDTIIFEA NGNLIAPRFA FALSRGFGSG IITSNAPMDE CDAKCQTPQG AINSSLPFQN VHPVTIGECP KYVRSAKLRM VTGLRNIPSI QSRGLFGAIA GFIEGGWTGM VDGWYGYHHQ NEQGSGYAAD QKSTQNAING ITNKVNSVIE KMNTQFTAVG KEFNKLERRM ENLNKKVDDG FLDIWTYNAE LLVLLENERT LDFHDSNVKN LYEKVKSQLK NNAKEIGNGC FEFYHKCNDE CMESVKNGTY DYPKYSEESK LNRERIDGVK LESMGVYQIL AIYSTVASSL VLLVSLGAIS FWMCSNGSLQ CRICI HEMAGGLUTININ [INFLUENZA A VIRUS (A/NEW YORK/483/2003(H1N1)) ACCESSION ABD15515 SEQ ID NO: 10 KVKLLVLLCT FTATYADTIC IGYHANNSTD TVDTVLEKNV TVTHSVNLLE DSHNGKLCLL KGIAPLQLGN CSVAGWILGN PECELLISKE SWSYIVETPN PENGTCYPGY FADYEELREQ LSSVSSFERF EIFPKESSWP NHTVTGVSAS CSHNGKSSFY RNLLWLTGKN GLYPNLSKSY ANNKEKEVLV LWGVHHPPNI GDQRALYHTE NAYISVVSSH YSRRFTPEIA KRPKVRDQEG RINYYWTLLE PGDTIIFEAN GNLIAPRYAF ALSRGFGSGI ITSNAPMDEC DAKCQTPQGA INSSLPFQNV HPVTIGECPK YVRSAKLRMV TGLRNIPSIQ SRGLFGAIAG FIEGGWTGMV DGWYGYHHQN EQGSGYAADQ KSTQNAINGI TNKVNSVIEK MNTQFTAVGK EFNKLERRME NLNKKVDDGF LDIWTYNAEL LVLLENERTL DFHDSNVKNL YEKVKSQLKN NAKEIGNGCF EFYHKCNDEC MESVKNGTYD YPRYSEESKL NREKIDGVKL ESMGVYQILA IYSTVASSLV LLVSLGAISF WMCSNGSLQC RICI HEMAGGLUTININ [INFLUENZA A VIRUS (A/BRISBANE/10/2007(H3N2))ACCESSION ABW23422 SEQ ID NO: 11 QKLPGNDNST ATLCLGHHAV PNGTIVKTIT NDQIEVTNAT ELVQSSSTGE ICDSPHQILD GENCTLIDAL LGDPQCDGFQ NKKWDLFVER SKAYSNCYPY DVPDYASLRS LVASSGTLEF NNESFNWTGV TQNGTSSACI RRSNNSFFSR LNWLTHLKFK YPALNVTMPN NEKFDKLYIW GVHHPGTDND QIFPYAQASG RITVSTKRSQ QTVIPNIGSR PRVRNIPSRI SIYWTIVKPG DILLINSTGN LIAPRGYFKI RSGKSSIMRS DAPIGKCNSE CITPNGSIPN DKPFQNVNRI TYGACPRYVK QNTLKLATGM RNVPEKQTRG IFGAIAGFIE NGWEGMVDGW YGFRHQNSEG IGQAADLKST QAAIDQINGK LNRLIGKTNE KFHQIEKEFS EVEGRIQDLE KYVEDTKIDL WSYNAELLVA LENQHTIDLT DSEMNKLFEK TKKQLRENAE DMGNGCFKIY HKCDNACIGS IRNGTYDHDV YRDEALNNRF QIKGVELKSG YKDWILWISF AISCFLLCVA LLGFIMWACQ KGNIRCNI HEMAGGLUTININ [INFLUENZA A VIRUS (A/WISCONSIN/34/2007(H3N2))ACCESSION ACB11766 SEQ ID NO: 12 MKTIIALSYI LCLVFAQKLP GNDNSTATLC LGHHAVPNGT IVKTITNDQI EVTNATELVQ SSSTGKICNS PHQILDGENC TLIDALLGDP QCDGFQNKKW DLFVERSKAS SNCYPYDVPD YASLRSLVAS SGTLEFNNES FNWTGVTQNG TSSACIRRSN NSFFSRLNWL THLKFKYPAL NVTMPNNEKF DKLYIWGVHH PGTDNDQIFL YAQATGRITV STKRSQQTVI PNIGSRPRVR NIPSRISIYW TIVKPGDIFL INSTGNLIAP RGYFKIQSGK SSIMRSDAPI GKCNSECITP NGSIPNDKPF QNVNRITYGA CPRYVKQNTL KLATGMRNVP EKQTRGIFGA IAGFIENGWE GMVDGWYGFR HQNSEGIGQA ADLKSTQAAI DQINGKLNRL IGKTNEKFHQ IEKEFSEVEG RIQDLEKYVE DTKIDLWSYN AELLVALENQ HTIDLTDSEM NKLFEKTKKQ LRENAEDMGN GCFKIYHKCD NACIGSIRNG TYDHDVYRDE ALNNRFQIKG IELKSGYKDW ILWISFAISC FLLCVALLGF IMWACQKGNI RCNICI HEMAGGLUTININ [INFLUENZA A VIRUS (A/MANAGUA/2/2007(H3N2))ACCESSION ACD85528, SEQ ID NO: 13 MKTIIALSYI LCLVFAQKLP GNDNSTATLC LGHHAVPNGT IVKTITNDQI EVTNATELVQ SSSTGEICDS PHQILDGENC TLIDALLGDP QCDGFQNKKW DLFVERSKAY SNCYPYDVPD YVSLRSLVAS SGTLEFNNES FNWTGVTQNG TSSACIRRSN KSFFSRLNWL THLKFKYPAL NVTMPNNENF DKLYIWGVHH PGTDNDQIFL YAQASGRITV STKRSQQTVI PNIGSRPRVR NIPSRISIYW TIVKPGDILL INSTGNLIAP RGYFKIRSGK SSIMRSDAPI GKCNSECITP NGSIPNDKPF QNVNRITYGA CPRYVKQNTL KLATGMRNVP EKQTRGIFGA IAGFIENGWE GMVDGWYGFR HQNSEGIGQA ADLKSTQAAI DQINGKLNRL IGKTNEKFHQ IEKEFSEVEG RIQDLEKYVE DTKIDLWSYN AELLVALENQ HTIDLTDSEM NKLFEKTKKQ LRENAEDLGN GCFKIYHKCD NACIGSIRNG TYDHDVYRDE ALNNRFQIKG VELKSGYKDW ILWISFAISC FLLCVALLGF IMWACQKGNI RCNICI hemagglutinin Influenza A virus HA1 subunit (A/Korea/426/68(H2N2)) (AA 3-345 out of 1-652 precursor) SEQ ID NO: 14 DQICIGYHAN NSTEKVDTIL ERNVTVTHAK DILEKTHNGK LCKLNGIPPL ELGDCSIAGW LLGNPECDRL LSVPEWSYIM EKENPRYSLC YPGSFNDYEE LKHLLSSVKH FEKVKILPKD RWTQHTTTGG SWACAVSGKP SFFRNMVWLT RKGSNYPVAK GSYNNTSGEQ MLIIWGVHHP NDEAEQRALY QNVGTYVSVA TSTLYKRSIP EIAARPKVNG LGRRMEFSWT LLDMWDTINF ESTGNLVAPE YGFKISKRGS SGIMKTEGTL ENCETKCQTP LGAINTTLPF HNVHPLTIGE CPKYVKSEKL VLATGLRNVP QIESR Hemagglutinin Influenza A virus full length (A/egret/Egypt/1162- NAMRU3/2006(H5N1)) SEQ ID NO: 15 QICIGYHANN STEQVDTIME KNVTVTHAQD ILEKTHNGKL CDLDGVKPLI LRDCSVAGWL LGNPMCDEFL NVPEWSYIVE KINPANDLCY PGNFNDYEEL KHLLSRINHF EKIQIIPKSS WSDHEASSGV SSACPYQGRS SFFRNVVWLI KKDNAYPTIK RSYNNTNQED LLVLWGIHHP NDAAEQTRLY QNPTTYISVG TSTLNQRLVP KIATRSKVNG QSGRMEFFWT ILKSNDAINF ESNGNFIAPE NAYKIVKKGD STIMKSELEY GNCNTKCQTP IGAINSSMPF HNIHPLTIGE CPKYVKSNRL VLATGLRNSP QGERRRKKRG LFGAIAGFIE GGWQGMVDGW YGYHHSNEQG SGYAADKEST QKAIDGVTNK VNSIIDKMNT QFEAVGREFN NLERRIENLN KKMEDGFLDV WTYNAELLVL MENERTLDFH DSNVKNLYDK VRLQLRDNAK ELGNGCFEFY HRCDNECMES VRNGTYDYPQ YSEEARLKRE EISGVKLESI GTYQILSIYS TVASSLALAI MVAGL INFLUENZA VIRUS M2 PROTEIN FROM TYPE A VIRUS (H5N1) ACCESSION NO. BAD89348 (AA 1-97) SEQ ID NO: 16 MSLLTEVETP TRNEWECRCS DSSDPLVVAA SIIGILHLIL WILDRLFFKC IYRRLKYGLK RGPSTAGVPE SMREEYRQEQ QSAVDVDDGH FVNIELE TRUNCATED ENVELOPE GLYCOPROTEIN HUMAN IMMUNODEFICIENCY VIRUS 2 ACCESSION ABC39624 SEQ ID NO: 17 AFLLTSACLI YCKQYVTVFY GIPAWKNASI PLFCATRNRD TWGTIQCLPD NDDYQEIVLN VAEAFDAWDN TVTEQAIEDV WNLFETSTKP CVKLTPLCVT MRCNTSTTTT TTAPTSTSAG STATPKPIMV NENTSCMHAN NCSGLGEEEV VNCEFNMTGL VRDKPKTYNE TWYSRDVDCE PDSTTNSRKC YMNHCNTSVI TESCDKHYWD DIRFRYCAPP GYALLRCNDT NYSGFAPNCS KVVASTCTRM METQTSTWFG FNGTRAENRT YLYWHSKSDR TIISLNKYYN LSIHCKRPGN KTVTPITLMS GYKFHSRPVI NTRPKQAWCW FKGRWKDAMQ EVKKTVAEHP RAVTKDPKNI TFAAPGKGSD PEVEYMWTNC RGEFLYCDMT WFLDWIENRP TRKAWRNYVP CHIRQIINTW HKVGKHVYLP PREGELTCNS TVTSIIANID VNEIDKRTNI TFSAEVAELY RVELGDYKLV EVTPIGFAPT SEKRYSSGHR ETYKRCARAR ILGFSRNSRF CNGRSVLDAV RSAPDFTGRD SAATATAVGR GQETTRNVAT DRLGNEKSPG KSHCYREIPK GSGAAKFMGM CV GP120 HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 ACCESSION AAF69492 SEQ ID NO: 18 VPVWRDADTT LFCASDAKSH VTEAHNVWAT HACVPTDPNP QEIHLENVTE NFNMWKNNMV EQMQEDVISL WEQSLKPCVK LTPLCVTLNC TNANLTNANL TNANNITNVE NITDEVRNCS FNVTTDLRDK QQKVHALFYR LDIVQINSKN SSDYRLINCN TSVIKQACPK ISFDPIPIHY CTPAGYAILK CNDKNFNGTG PCKNVSSVQC THGIKPVVST QLLLNGSLAE EEIIIRSENL TNNVKTIIVH LNKSVEINCT RPSNNTRTSI TIGPGQVFYR TGDIIGDIRK VSCELNGTKW NEVLKQVKEK LKEHFNKNIS FQPPSGGDLE ITMHHFSCRG EFFYCNTTQL FNNTYSNGTI TLPCKIKQII NMWQGVGQAM YAPPISGRIN CLSNITGLLL TRDGNNGTNE TFRPGGGNIK DNWRSELYKC KVVQIEPLGI APTRAKRRVV EREKK ENVELOPE GLYCOPROTEIN I HUMAN HERPESVIRUS 3 ACCESSION NP_040189 SEQ ID NO: 19 MFLIQCLISA VIFYIQVTNA LIFKGDHVSL QVNSSLTSIL IPMQNDNYTE IKGQLVFIGE QLPTGTNYSG TLELLYADTV AFCFRSVQVI RYDGCPRIRT SAFISCRYKH SWHYGNSTDR ISTEPDAGVM LKITKPGIND AGVYVLLVRL DHSRSTDGFI LGVNVYTAGS HHNIHGVIYT SPSLQNGYST RALFQQARLC DLPATPKGSG TSLFQHMLDL RAGKSLEDNP WLHEDVVTTE TKSVVKEGIE NHVYPTDMST LPEKSLNDPP ENLLIIIPIV ASVMILTAMV IVIVISVKRR RIKKHPIYRP NTKTRRGIQN ATPESDVMLE AAIAQLATIR EESPPHSVVN PFVK 

1. A process for manufacturing a composition comprising directed-sequence polymers (DSPs) useful for eliciting immune responses in a subject, comprising the steps of: (a) selecting a first base peptide sequence, wherein the sequence is an amino acid sequence of an epitope of an antigen associated with a disease treatable by or preventable by vaccination against the epitope and wherein the length of the sequence is 6 to 75; (b) synthesizing by solid-phase peptide synthesis a first cassette of the DSPs, such cassette having a length of at least 8 amino acids and fewer than 75 amino acids, wherein, for each sequential amino acid position of the first cassette, an amino acid is sequentially incorporated into the DSP, such amino acid for each said position randomly selected from a mixture of amino acids consisting of: (i) an original amino acid, which is an amino acid found at said amino acid position in said first peptide sequence, such original amino acid present in the pool at a relative molar concentration of a0; (ii) optionally one or more replacement of the original amino acid, said replacement defined according to amino acid similarity to the original amino acid or selected from amino acids found as naturally occurring variations in a corresponding position in a protein having the same or substantially the same physiological role and/or activity as the antigen, such position corresponding to said amino acid position, each such replacement amino acid present in the mixture at a relative molar concentration of aN wherein N is an integer unique to each such replacement amino acid; and (iii) A: alanine, present in the mixture at a fixed relative molar concentration A, wherein the amino acids in the mixture are present in a fixed molar input ratio relative to each other, determined prior to starting synthesis, wherein the relative molar amount of A is more than 10% and less than 90% of the total amino acid concentration of the DSPs, and a0 is within the range of 0.05-50%, each of aN is within the range of 0-50%, and wherein all fractional concentrations of amino acids add up to 100%; (c) optionally further extending the length of the DSPs by selecting a step from the group consisting of: (i) repeating step (b) for 2 to 15 cycles and elongating the DSP under the same condition including the input ratio of amino acids in the mixture; (ii) repeating step (b) for 2 to 15 cycles and elongating the DSP, for each cycle, using a different input ratio of amino acids in the mixture; (iii) repeating steps (a) and (b) for 2 to 15 cycles and elongating the DSP using cassettes based on more than one base peptide; (iv) assembling 2 to 15 cassettes synthesized in a single cycle of step (b); and (v) assembling 2 to 15 cassettes, the first cassette synthesized under one condition of step (b), and second and more cassettes synthesized under one or more different conditions of step (b); wherein the number of cycles selected in step (c) is selected so that the final length of the DSP is about 25 to 300 amino acid residues.
 2. The process according to claim 1, wherein the first base peptide sequence is selected from a group consisting of SEQ ID NO: 1 through 7 and a known epitope sequence which is a partial sequence of SEQ ID NO: 8 through
 19. 3. The process according to claim 1, wherein the immune response derives from a host's infection by a pathogen.
 4. The process according to claim 3, wherein the pathogen is a virus.
 5. The process according to claim 4, wherein the virus is an influenza virus.
 6. The process according to claim 3, wherein the pathogen is a parasite.
 7. The process according to claim 4, wherein the infection results in a disease selected from the group consisting of AIDS, AIDS Related Complex, Chickenpox (Varicella), Common cold, Cytomegalovirus Infection, Colorado tick fever, Dengue fever, Ebola haemorrhagic fever, Hand, foot and mouth disease, Hepatitis, Herpes simplex, Herpes zoster, HPV, Influenza (Flu), Lassa fever, Measles, Marburg haemorrhagic fever, Infectious mononucleosis, Mumps, Poliomyelitis, Progressive multifocal leukencephalopathy, Rabies, Rubella, SARS, Smallpox (Variola), Viral encephalitis, Viral gastroenteritis, Viral meningitis, Viral pneumonia, West Nile disease, and Yellow fever.
 8. The process according to claim 1, wherein the final average length of DSPs is between about 45 and about 70 residues.
 9. The process according to claim 1, wherein the relative molar concentration of alanine in the final DSP composition is between about 15% and 70%.
 10. The process according to claim 12, wherein the relative molar concentration of alanine in the final DSP composition is between about 20% and 50%.
 11. A composition comprising directed-sequence polymers (DSPs) manufactured by the process according to claim
 1. 12. A composition comprising directed-sequence polymers (DSPs) having a length of between about 25 to 300 amino acids, wherein each of such DSPs comprises between 1-15 cassettes, each cassette comprising between 8-70 amino acids; wherein each cassette is derived from a first base peptide sequence, wherein the sequence is an amino acid sequence of an epitope of an antigen associated with a disease treatable by or preventable by vaccination against the epitope, and the amino acid at each position of the cassette is selected from the group consisting of: (a) an amino acid, a0, found at the corresponding position in a first base peptide sequence; (b) optionally a replacement, if applicable, of the amino acid, a1, found at the said position in said selected amino acid sequence, said primary replacement defined according to amino acid similarity or selected from an amino acid found as a naturally occurring variation in a corresponding position to said position in a protein having the same or substantially the same physiological role and/or activity as the antigen, each such replacement amino acid present in the mixture at a relative molar concentration of aN wherein N is an integer unique to each such replacement amino acid; and (c) A: alanine; wherein the amino acids in the mixture are present in a fixed molar input ratio relative to each other, and wherein the relative molar amount of A is at least 20% of the total amino acid comprising the DSPs, and all fractional ratios of amino acids add up to 100%.
 13. The composition of claim 12, wherein said DSP comprises cassettes, such cassettes comprising the amino acid sequences that are derived from the first base peptide sequence.
 14. The composition of claim 12, wherein said DSP comprises one or more cassettes, such cassettes comprising one or more cassettes having amino acid sequences that are derived from the first base peptide sequence and one or more cassettes having amino acid sequences that are derived from a second base peptide sequence of a second epitope.
 15. The composition of claim 12, wherein the first base peptide sequence is selected from SEQ ID NO:1-7.
 16. The composition of claim 12, wherein the disease is selected from the group consisting of viral infection, bacterial infection, and parasitic infection.
 17. The composition of claim 12, wherein the amino acid similarity is defined according to the similarity table shown in FIG.
 4. 18. The composition of claim 12, wherein the amino acid similarity is determined based on empirical data of known variants of the epitope.
 19. A method of treating an infectious disease by administering to a subject in need thereof a composition comprising directed-sequence polymers (DSPs), comprising administering to the subject a dosing regimen of an effective amount of the DSP composition selected from any one of claims 14 to 20 to elicit immune responses in the subject, wherein said immune responses ameliorates symptoms of said disease.
 20. The method according to claim 19, wherein the infectious disease is selected from the group consisting of viral infection, bacterial infection, and parasitic infection.
 21. The method according to claim 19, wherein the subject's naturally occurring immune response to the antigen is inadequate for preventing or overcoming the pathology associated with the antigen for which the immune response is elicited.
 22. A method of protecting a subject from an influenza virus infection wherein the influenza virus is a new immunologic subtype, such method comprising the step of administering a pharmaceutical composition comprising a DSP composition, the base sequence of which comprises a variable epitope region determined by analyzing amino acid structure variations within the most recent cluster.
 23. A method of protecting a subject from an influenza virus infection comprising the steps of administering a pharmaceutical composition comprising a DSP composition, the base sequence of which comprises a variable epitope region of a hemagglutinin sequence of a strain determined by the World Health Organization as a variant likely to be prevalent for an upcoming season for which such protection is sought.
 24. The method of claim 23, wherein the variant is predicted to be prevalent in Northern Hemisphere.
 25. A method of protecting a subject from an influenza virus infection wherein the infecting virus is resides within an inter-pandemic cluster, such method comprising the step of administering a pharmaceutical composition comprising a DSP composition, the base sequence of which derives from variable epitope regions of an influenza protein, determined by identifying amino acid variations within said inter-pandemic cluster.
 26. The method of claim 25, wherein the variable epitope regions reside within hemagglutinin.
 27. The method of claim 25, wherein the virus is further defined as having been selected by the World Health organization as a new vaccination strain.
 28. A method of preparing a subject for an influenza virus infection wherein the infecting virus is resides within an newly dominant cluster, such method comprising the step of administering a pharmaceutical composition comprising a DSP composition, the base sequence of which derives from variable epitope regions of hemagglutinin determined by identifying amino acid variations within an inter-pandemic cluster.
 29. Use of a composition according to any one of claims 12 to 18 for the manufacture of a medicament for the treatment of an infectious disease. 